diff --git a/lib/miga/cli/action/add_result.rb b/lib/miga/cli/action/add_result.rb
index 20504f50..63194aa0 100644
--- a/lib/miga/cli/action/add_result.rb
+++ b/lib/miga/cli/action/add_result.rb
@@ -5,13 +5,17 @@
 
 class MiGA::Cli::Action::AddResult < MiGA::Cli::Action
   def parse_cli
-    cli.defaults = { force: false }
+    cli.defaults = { force: false, stdin_versions: false }
     cli.parse do |opt|
       cli.opt_object(opt, [:project, :dataset_opt, :result])
       opt.on(
         '-f', '--force',
         'Force re-indexing of the result even if it\'s already registered'
       ) { |v| cli[:force] = v }
+      opt.on(
+        '--stdin-versions',
+        'Read Software versions from STDIN'
+      ) { |v| cli[:stdin_versions] = v }
     end
   end
 
@@ -21,5 +25,22 @@ def perform
     cli.say "Registering result: #{cli[:result]}"
     r = obj.add_result(cli[:result], true, force: cli[:force])
     raise 'Cannot add result, incomplete expected files' if r.nil?
+
+    # Add Software version data
+    if cli[:stdin_versions]
+      versions = {}
+      sw = nil
+      $stdin.each do |ln|
+        ln = ln.chomp.strip
+        if ln =~ /^=> (.*)/
+          sw = $1
+          versions[sw] = ''
+        else
+          versions[sw] += ln
+        end
+      end
+      r.add_versions(versions)
+      r.save
+    end
   end
 end
diff --git a/lib/miga/cli/action/download/gtdb.rb b/lib/miga/cli/action/download/gtdb.rb
index 9a70f1d1..10ed5706 100644
--- a/lib/miga/cli/action/download/gtdb.rb
+++ b/lib/miga/cli/action/download/gtdb.rb
@@ -31,7 +31,7 @@ def sanitize_cli
 
   def remote_list
     cli.say 'Downloading genome list'
-    extra = ['sp_reps_only=' + cli[:reference].to_s]
+    extra = { sp_reps_only: cli[:reference].to_s }
     json = MiGA::RemoteDataset.download(
       :gtdb, :taxon, cli[:taxon], :genomes, nil, extra
     )
diff --git a/lib/miga/cli/action/download/ncbi.rb b/lib/miga/cli/action/download/ncbi.rb
index 0248fa54..238b799c 100644
--- a/lib/miga/cli/action/download/ncbi.rb
+++ b/lib/miga/cli/action/download/ncbi.rb
@@ -34,11 +34,8 @@ def cli_name_modifiers(opt)
       'Do not add sequence version to the dataset name',
       'Only affects --complete and --chromosome'
     ) { |v| cli[:add_version] = v }
-    cli.opt_flag(
-      opt, 'legacy-name',
-      'Use dataset names based on chromosome entries instead of assembly',
-      :legacy_name
-    )
+    # For backwards compatibility
+    cli.opt_flag(opt, 'legacy-name', '::HIDE::', :legacy_name)
   end
 
   def sanitize_cli
@@ -52,89 +49,67 @@ def sanitize_cli
   end
 
   def remote_list
-    doc =
-      if cli[:ncbi_table_file]
-        cli.say 'Reading genome list from file'
-        File.open(cli[:ncbi_table_file], 'r')
-      else
-        cli.say 'Downloading genome list'
-        url = remote_list_url
-        MiGA::RemoteDataset.download_url(url)
-      end
-    ds = parse_csv_as_datasets(doc)
-    doc.close if cli[:ncbi_table_file]
-    ds
+    list  = {}
+    query = remote_list_query
+    loop do
+      # Query the remote collection
+      page = MiGA::Json.parse(
+        MiGA::RemoteDataset.download(:ncbi_datasets, :genome, query, :json),
+        contents: true
+      )
+      break unless page&.any? && page[:reports]&.any?
+
+      # Process reports in this page
+      list.merge!(parse_reports_as_datasets(page[:reports]))
+
+      # Next page
+      break unless page[:next_page_token]
+      query[:page_token] = page[:next_page_token]
+    end
+    list
   end
   
-  def parse_csv_as_datasets(doc)
+  def parse_reports_as_datasets(reports)
     ds = {}
-    CSV.parse(doc, headers: true).each do |r|
-      asm = r['assembly']
+    reports.each do |r|
+      asm = r[:accession]
       next if asm.nil? || asm.empty? || asm == '-'
 
-      rep = remote_row_replicons(r)
-      n = remote_row_name(r, rep, asm)
-
       # Register for download
+      n = remote_report_name(r, asm)
       ds[n] = {
         ids: [asm], db: :assembly, universe: :ncbi,
         md: {
-          type: :genome, ncbi_asm: asm, strain: r['strain']
+          type: :genome, ncbi_asm: asm, strain: r.dig(:organism, :infraspecific_names, :strain)
         }
       }
-      ds[n][:md][:ncbi_nuccore] = rep.join(',') unless rep.nil?
-      unless r['release_date'].nil?
-        ds[n][:md][:release_date] = Time.parse(r['release_date']).to_s
-      end
+      date = r.dig(:assembly_info, :release_date)
+      ds[n][:md][:release_date] = Time.parse(date).to_s if date
+      ds[n][:md][:ncbi_dataset] = r
     end
     ds
   end
 
-  def remote_row_replicons(r)
-    return if r['replicons'].nil?
-
-    r['replicons']
-      .split('; ')
-      .map { |i| i.gsub(/.*:/, '') }
-      .map { |i| i.gsub(%r{/.*}, '') }
-  end
-
-  def remote_row_name(r, rep, asm)
-    return r['#organism'].miga_name if cli[:legacy_name] && cli[:reference]
-
-    if cli[:legacy_name] && ['Complete', ' Chromosome'].include?(r['level'])
-      acc = rep.nil? ? '' : rep.first
-    else
-      acc = asm
-    end
+  def remote_report_name(r, asm)
+    acc = "#{asm}"
     acc.gsub!(/\.\d+\Z/, '') unless cli[:add_version]
-    "#{r['#organism']}_#{acc}".miga_name
+    org = r.dig(:organism, :organism_name)
+    acc = "#{org}_#{acc}" if org
+    acc.miga_name
   end
 
-  def remote_list_url
-    url_base = 'https://www.ncbi.nlm.nih.gov/genomes/solr2txt.cgi?'
-    url_param = {
-      q: '[display()].' \
-        'from(GenomeAssemblies).' \
-        'usingschema(/schema/GenomeAssemblies).' \
-        'matching(tab==["Prokaryotes"] and q=="' \
-          "#{cli[:taxon]&.tr('"', "'")}\"",
-      fields: 'organism|organism,assembly|assembly,replicons|replicons,' \
-        'level|level,release_date|release_date,strain|strain',
-      nolimit: 'on'
-    }
+  def remote_list_query
+    q = { taxons: [cli[:taxon]], filters: {} }
     if cli[:reference]
-      url_param[:q] += ' and refseq_category==["representative"]'
+      q[:filters][:reference_only] = true
     else
-      status = {
-        complete: 'Complete',
-        chromosome: ' Chromosome', # <- The leading space is *VERY* important!
-        scaffold: 'Scaffold',
-        contig: 'Contig'
-      }.map { |k, v| '"' + v + '"' if cli[k] }.compact.join(',')
-      url_param[:q] += ' and level==[' + status + ']'
+      q[:assembly_level] = {
+        contig: 'contig',
+        scaffold: 'scaffold',
+        chromosome: 'chromosome',
+        complete: 'complete_genome'
+      }.map { |k, v| '"' + v + '"' if cli[k] }.compact
     end
-    url_param[:q] += ')'
-    url_base + URI.encode_www_form(url_param)
+    q
   end
 end
diff --git a/lib/miga/cli/action/download/seqcode.rb b/lib/miga/cli/action/download/seqcode.rb
index 0696d5fd..087f505b 100644
--- a/lib/miga/cli/action/download/seqcode.rb
+++ b/lib/miga/cli/action/download/seqcode.rb
@@ -29,8 +29,7 @@ def remote_list
 
     while current_page <= total_pages
       json = MiGA::RemoteDataset.download(
-        :seqcode, :'type-genomes', nil, :json, nil,
-        ["page=#{current_page}"]
+        :seqcode, :'type-genomes', nil, :json, nil, page: current_page
       )
       doc = MiGA::Json.parse(json, contents: true)
       current_page = doc[:current_page] + 1
diff --git a/lib/miga/cli/action/ncbi_get.rb b/lib/miga/cli/action/ncbi_get.rb
index d58c5380..859bcc3a 100644
--- a/lib/miga/cli/action/ncbi_get.rb
+++ b/lib/miga/cli/action/ncbi_get.rb
@@ -8,8 +8,7 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
 
   def parse_cli
     cli.defaults = {
-      query: false, unlink: false,
-      reference: false, legacy_name: false,
+      query: false, unlink: false, reference: false,
       complete: false, chromosome: false,
       scaffold: false, contig: false, add_version: true, dry: false,
       get_md: false, only_md: false, save_every: 1
@@ -29,12 +28,6 @@ def parse_cli
         '--api-key STRING',
         '::HIDE::' # For backwards compatibility
       ) { |v| ENV['NCBI_API_KEY'] = v }
-      opt.on(
-        '--ncbi-table-file STRING',
-        '::HIDE::' # Only meant for debugging
-        # It can take the table returned by NCBI and parse it from a file
-        # instead of downloading it directly
-      ) { |v| cli[:ncbi_table_file] = v }
       opt.on(
         '--ncbi-api-key STRING',
         'NCBI API key'
diff --git a/lib/miga/cli/action/wf.rb b/lib/miga/cli/action/wf.rb
index 2ad7375e..1265e570 100644
--- a/lib/miga/cli/action/wf.rb
+++ b/lib/miga/cli/action/wf.rb
@@ -8,7 +8,8 @@ def default_opts_for_wf
     cli.expect_files = true
     cli.defaults = {
       clean: false, project_type: :genomes, dataset_type: :popgenome,
-      ncbi_draft: true, min_qual: MiGA::Project.OPTIONS[:min_qual][:default],
+      ncbi_draft: true, ncbi_ref: false,
+      min_qual: MiGA::Project.OPTIONS[:min_qual][:default],
       prepare_and_exit: false
     }
   end
@@ -39,14 +40,21 @@ def opts_for_wf(opt, files_desc, params = {})
         '-T', '--ncbi-taxon STRING',
         'Download all the genomes in NCBI classified as this taxon'
       ) { |v| cli[:ncbi_taxon] = v }
+      opt.on(
+        '--no-draft', '::HIDE::' # Deprecated
+      ) { |v| cli[:ncbi_draft] = v }
+      opt.on(
+        '--ncbi-complete',
+        'Only download complete genomes, not drafts (requires -T)'
+      ) { |v| cli[:ncbi_draft] = !v }
+      opt.on(
+        '--ncbi-ref',
+        'Only download RefSeq reference genomes (requires -T)'
+      ) { |v| cli[:ncbi_ref] = v }
       opt.on(
         '-G', '--gtdb-taxon STRING',
         'Download all the genomes in GTDB classified as this taxon'
       ) { |v| cli[:gtdb_taxon] = v }
-      opt.on(
-        '--no-draft',
-        'Only download complete genomes, not drafts (requires -T)'
-      ) { |v| cli[:ncbi_draft] = v }
       opt.on(
         '--gtdb-ref',
         'Only download reference anchor genomes in GTDB (requires -G)'
@@ -170,7 +178,8 @@ def initialize_empty_project(metadata)
   def download_datasets
     # Download datasets from NCBI
     unless cli[:ncbi_taxon].nil?
-      what = cli[:ncbi_draft] ? '--all' : '--complete'
+      what = cli[:ncbi_ref] ? '--reference' :
+             cli[:ncbi_draft] ? '--all' : '--complete'
       cmd = ['ncbi_get', '-P', cli[:outdir], '-T', cli[:ncbi_taxon], what]
       cmd += ['--max', cli[:max_download]] if cli[:max_download]
       call_cli(cmd)
diff --git a/lib/miga/cli/objects_helper.rb b/lib/miga/cli/objects_helper.rb
index d28e6f62..abda3213 100644
--- a/lib/miga/cli/objects_helper.rb
+++ b/lib/miga/cli/objects_helper.rb
@@ -60,6 +60,9 @@ def load_and_filter_datasets(silent = false)
       o &&= (d.ref? == self[:ref]) unless self[:ref].nil?
       o &&= (d.active? == self[:active]) unless self[:active].nil?
       o &&= (self[:multi] ? d.multi? : d.nonmulti?) unless self[:multi].nil?
+      unless self[:markers].nil?
+        o &&= (self[:markers] ? d.markers? : !d.markers?)
+      end
       unless self[:taxonomy].nil?
         o &&= !d.metadata[:tax].nil? && d.metadata[:tax].in?(self[:taxonomy])
       end
diff --git a/lib/miga/cli/opt_helper.rb b/lib/miga/cli/opt_helper.rb
index e4d6c546..1a44e322 100644
--- a/lib/miga/cli/opt_helper.rb
+++ b/lib/miga/cli/opt_helper.rb
@@ -43,7 +43,7 @@ def opt_common(opt)
       '-h', '--help',
       'Display this screen'
     ) do
-      puts opt.to_s.gsub(/^.*\s+::HIDE::\s*$/, '')
+      puts opt.to_a.select { |i| i !~ /\s::HIDE::\s/ }
       exit
     end
     opt.separator ''
@@ -120,10 +120,11 @@ def opt_object(opt, what = %i[project dataset])
   # as determined by +what+ an Array with any combination of:
   # - :ref To filter by reference (--ref) or query (--no-ref)
   # - :multi To filter by multiple (--multi) or single (--no-multi) species
+  # - :markers To filter by with (--markers) or without markers (--no-markers)
   # - :active To filter by active (--active) or inactive (--no-active)
   # - :taxonomy To filter by taxonomy (--taxonomy)
   # The "k-th" filter (--dataset-k) is always included
-  def opt_filter_datasets(opt, what = %i[ref multi active taxonomy])
+  def opt_filter_datasets(opt, what = %i[ref multi markers active taxonomy])
     what.each do |w|
       case w
       when :ref
@@ -136,6 +137,11 @@ def opt_filter_datasets(opt, what = %i[ref multi active taxonomy])
           '--[no-]multi',
           'Use only multi-species (or only single-species) datasets'
         ) { |v| self[:multi] = v }
+      when :markers
+        opt.on(
+          '--[no-]markers',
+          'Use only datasets with (or without) markers'
+        ) { |v| self[:markers] = v }
       when :active
         opt.on(
           '--[no-]active',
diff --git a/lib/miga/common/net.rb b/lib/miga/common/net.rb
index a2477497..bb903676 100644
--- a/lib/miga/common/net.rb
+++ b/lib/miga/common/net.rb
@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require 'net/http'
 require 'net/ftp'
 require 'open-uri'
 require 'fileutils'
@@ -10,6 +11,8 @@
 ##
 # General web-access functions shared throughout MiGA.
 module MiGA::Common::Net
+  attr_accessor :remote_connection_uri
+
   ##
   # Returns the URL of the host +name+ (Symbol)
   def known_hosts(name)
@@ -21,7 +24,7 @@ def known_hosts(name)
     when :miga_dist
       "ftp://#{main_server}/dist"
     else
-      raise "Unrecognized server name: #{host}"
+      raise "Unrecognized server name: #{name}"
     end
   end
 
@@ -32,49 +35,128 @@ def main_server
   end
 
   ##
-  # Connect to an FTP +host+ (String) or a known host name (Symbol, see
-  # +.known_hosts+)
+  # Connect to an FTP +host+ (String), a known host name (Symbol, see
+  # +.known_hosts+), or a parsed +URI+ object
+  #
+  # Sets the attribute +remote_connection_uri+ to the parsed +URI+ object
+  # silently
   def remote_connection(host)
     host = known_hosts(host) if host.is_a?(Symbol)
-    uri = URI.parse(host)
-    raise 'Only FTP hosts are currently supported' unless uri.scheme == 'ftp'
-
-    ftp = Net::FTP.new(uri.host)
-    ftp.passive = true
-    ftp.login
-    ftp.chdir(uri.path)
-    ftp
+    uri = host.is_a?(URI) ? host : URI.parse(host)
+    @remote_connection_uri = uri
+
+    case uri.scheme
+    when 'ftp'
+      ftp = Net::FTP.new(uri.host)
+      ftp.passive = true
+      ftp.login
+      ftp.chdir(uri.path) unless host.is_a?(URI)
+      ftp
+    when 'http', 'https'
+      http = Net::HTTP.new(uri.host, uri.port)
+      http.read_timeout = 600
+      http.use_ssl = uri.scheme == 'https'
+      http
+    else
+      raise 'Only FTP, HTTP, and HTTPS are currently supported'
+    end
   end
 
   ##
   # Download a file via FTP using the +connection+ (returned by
-  # +.remote_connection+) with remote name +file+ into local +target+.
+  # +.remote_connection+) with remote name +file+ into local +target+. If +file+
+  # is +nil+, it tries to guess the file from +connection+. If +target+ is
+  # +nil+, it returns the read data instead
   #
-  # Alternatively, +connection+ can simply be the host (String) or a recognized
-  # Symbol (see +.remote_connection+), in which case the function opens the
-  # connection automatically
+  # Alternatively, +connection+ can simply be the host (String), a recognized
+  # Symbol (see +.remote_connection+), or a parsed +URI+ object, in which case
+  # the function opens the connection automatically
   #
   # Reports progress to the function block with two arguments: the
   # currently transferred size and the total file size
-  def download_file_ftp(connection, file, target)
+  def download_file_ftp(connection, file = nil, target = nil)
     # Open connection unless passed
     close_conn = false
-    if connection.is_a?(String) || connection.is_a?(Symbol)
+    if connection.is_a?(String) || connection.is_a?(Symbol) ||
+          connection.is_a?(URI)
       connection = remote_connection(connection)
+      file ||= remote_connection_uri.path
       close_conn = true
     end
 
     # Prepare download
-    FileUtils.mkdir_p(File.dirname(target))
+    FileUtils.mkdir_p(File.dirname(target)) if target
     filesize = connection.size(file)
     transferred = 0
 
     # Get in chunks of 1KiB
+    ret = ''
     connection.getbinaryfile(file, target, 1024) do |data|
       yield(transferred += data.size, filesize) if block_given?
+      ret += data unless target
     end
 
     # Close connection if automatically opened
     connection.close if close_conn
+    ret unless target
+  end
+
+  ##
+  # Submit an HTTP or HTTPS request using +url+, which should be a URL
+  # either as String or parsed URI. The request follows the +method+, which
+  # should be a Net::HTTP verb such as +:get+, +:post+, or +:patch+. All
+  # additional parameters for the corresponding method should be passed as
+  # +opts+.
+  def http_request(method, url, *opts)
+    doc = nil
+    remote_connection(url).start do |http|
+      res = http.send(method, remote_connection_uri.to_s, *opts)
+      if %w[301 302].include?(res.code)
+        DEBUG "REDIRECTION #{res.code}: #{res['location']}"
+        return http_request(method, res['location'], *opts)
+      end
+      res.value # To force exception unless success
+      doc = res.body
+    end
+    doc
+  end
+
+  def net_method(method, uri, *opts)
+    attempts ||= 0
+    DEBUG "#{method.to_s.upcase}: #{uri} #{opts}"
+    case method.to_sym
+    when :ftp
+      download_file_ftp(uri)
+    else
+      http_request(method, uri, *opts)
+    end
+  rescue => e
+    raise e if (attempts += 1) >= 3
+
+    sleep 5 # <- For: 429 Too Many Requests
+    DEBUG "RETRYING after: #{e}"
+    retry
+  end
+
+  alias :https_request :http_request
+
+  ##
+  # Normalize the encoding of +body+ to UTF-8 by attempting several
+  # common recodings. Code from https://github.com/seq-code/registry
+  def normalize_encoding(body)
+    # Test encodings
+    body.force_encoding('utf-8')
+    %w[iso8859-1 windows-1252 us-ascii ascii-8bit].each do |enc|
+      break if body.valid_encoding?
+      recode = body.force_encoding(enc).encode('utf-8')
+      body = recode if recode.valid_encoding?
+    end
+    # If nothing works, replace offending characters with '?'
+    unless body.valid_encoding?
+      body = body.encode(
+        'utf-8', invalid: :replace, undef: :replace, replace: '?'
+      )
+    end
+    body
   end
 end
diff --git a/lib/miga/dataset.rb b/lib/miga/dataset.rb
index b373091d..40ad40f5 100644
--- a/lib/miga/dataset.rb
+++ b/lib/miga/dataset.rb
@@ -6,6 +6,7 @@
 require 'miga/metadata'
 require 'miga/dataset/result'
 require 'miga/dataset/status'
+require 'miga/dataset/type'
 require 'miga/dataset/hooks'
 
 # This library is only required by +#closest_relatives+, so it is now
@@ -18,6 +19,7 @@
 class MiGA::Dataset < MiGA::MiGA
   include MiGA::Dataset::Result
   include MiGA::Dataset::Status
+  include MiGA::Dataset::Type
   include MiGA::Dataset::Hooks
 
   # Class-level
@@ -56,6 +58,7 @@ def initialize(project, name, is_ref = true, metadata = {})
             name.to_s
     @project, @name, @metadata = project, name, nil
     metadata[:ref] = is_ref
+    metadata[:type] ||= :empty
     @metadata_future = [
       File.join(project.path, 'metadata', "#{name}.json"),
       metadata
@@ -89,12 +92,6 @@ def save
   # +Project+ interface
   alias :save! :save
 
-  ##
-  # Get the type of dataset as Symbol
-  def type
-    metadata[:type]
-  end
-
   ##
   # Delete the dataset with all it's contents (including results) and returns
   # nil
@@ -146,22 +143,6 @@ def query?
     !metadata[:ref]
   end
 
-  ##
-  # Is this dataset known to be multi-organism?
-  def multi?
-    return false if metadata[:type].nil? || @@KNOWN_TYPES[type].nil?
-
-    @@KNOWN_TYPES[type][:multi]
-  end
-
-  ##
-  # Is this dataset known to be single-organism?
-  def nonmulti?
-    return false if metadata[:type].nil? || @@KNOWN_TYPES[type].nil?
-
-    !@@KNOWN_TYPES[type][:multi]
-  end
-
   ##
   # Is this dataset active?
   def active?
diff --git a/lib/miga/dataset/base.rb b/lib/miga/dataset/base.rb
index 51d7b422..c6e52977 100644
--- a/lib/miga/dataset/base.rb
+++ b/lib/miga/dataset/base.rb
@@ -32,6 +32,12 @@ def EXCLUDE_NOREF_TASKS
       @@EXCLUDE_NOREF_TASKS
     end
 
+    ##
+    # Tasks to be excluded from datasets without markers
+    def EXCLUDE_NOMARKER_TASKS
+      @@EXCLUDE_NOMARKER_TASKS
+    end
+
     ##
     # Tasks to be executed only in datasets that are single-organism. These
     # tasks are ignored for multi-organism datasets or for unknown types
@@ -81,45 +87,67 @@ module MiGA::Dataset::Base
   # Supported dataset types
   @@KNOWN_TYPES = {
     genome: {
-      description: 'The genome from an isolate', multi: false
+      description: 'The genome from an isolate',
+      multi: false, markers: true,
+      project_types: %i[mixed genomes clade]
     },
     scgenome: {
-      description: 'A Single-cell Amplified Genome (SAG)', multi: false
+      description: 'A Single-cell Amplified Genome (SAG)',
+      multi: false, markers: true,
+      project_types: %i[mixed genomes clade]
     },
     popgenome: {
-      description: 'A Metagenome-Assembled Genome (MAG)', multi: false
+      description: 'A Metagenome-Assembled Genome (MAG)',
+      multi: false, markers: true,
+      project_types: %i[mixed genomes clade]
     },
     metagenome: {
-      description: 'A metagenome (excluding viromes)', multi: true
+      description: 'A metagenome (excluding viromes)',
+      multi: true, markers: true,
+      project_types: %i[mixed metagenomes]
     },
     virome: {
-      description: 'A viral metagenome', multi: true
+      description: 'A viral metagenome',
+      multi: true,
+      markers: true, # <- We don't expect, but can be useful for contamination
+      project_types: %i[mixed metagenomes]
+    },
+    plasmid: {
+      description: 'An individual plasmid',
+      multi: false, markers: false,
+      project_types: %i[mixed plasmids]
     }
   }
 
   ##
   # Returns an Array of tasks (Symbols) to be executed before project-wide tasks
-  @@PREPROCESSING_TASKS = [
-    :raw_reads, :trimmed_reads, :read_quality, :trimmed_fasta,
-    :assembly, :cds, :essential_genes, :mytaxa, :mytaxa_scan,
-    :taxonomy, :distances, :ssu, :stats
+  @@PREPROCESSING_TASKS = %i[
+    raw_reads trimmed_reads read_quality trimmed_fasta
+    assembly cds essential_genes mytaxa mytaxa_scan
+    taxonomy distances ssu stats
   ]
 
   ##
   # Tasks to be excluded from query datasets
-  @@EXCLUDE_NOREF_TASKS = [:mytaxa_scan, :taxonomy]
+  @@EXCLUDE_NOREF_TASKS = %i[mytaxa_scan taxonomy]
   @@_EXCLUDE_NOREF_TASKS_H = Hash[@@EXCLUDE_NOREF_TASKS.map { |i| [i, true] }]
 
+  ##
+  # Tasks to be excluded from datasets without markers
+  @@EXCLUDE_NOMARKER_TASKS = %i[essential_genes ssu]
+  @@_EXCLUDE_NOMARKER_TASKS_H =
+    Hash[@@EXCLUDE_NOMARKER_TASKS.map { |i| [i, true] }]
+
   ##
   # Tasks to be executed only in datasets that are single-organism. These
   # tasks are ignored for multi-organism datasets or for unknown types
-  @@ONLY_NONMULTI_TASKS = [:mytaxa_scan, :taxonomy, :distances]
+  @@ONLY_NONMULTI_TASKS = %i[mytaxa_scan taxonomy distances]
   @@_ONLY_NONMULTI_TASKS_H = Hash[@@ONLY_NONMULTI_TASKS.map { |i| [i, true] }]
 
   ##
   # Tasks to be executed only in datasets that are multi-organism. These
   # tasks are ignored for single-organism datasets or for unknwon types
-  @@ONLY_MULTI_TASKS = [:mytaxa]
+  @@ONLY_MULTI_TASKS = %i[mytaxa]
   @@_ONLY_MULTI_TASKS_H = Hash[@@ONLY_MULTI_TASKS.map { |i| [i, true] }]
 
   ##
diff --git a/lib/miga/dataset/hooks.rb b/lib/miga/dataset/hooks.rb
index b3fc40c5..c3e3ae5a 100644
--- a/lib/miga/dataset/hooks.rb
+++ b/lib/miga/dataset/hooks.rb
@@ -15,6 +15,7 @@
 # Supported hooks:
 # - run_lambda(lambda, args...)
 # - recalculate_status()
+# - check_type()
 # - clear_run_counts()
 # - run_cmd(cmd)
 # Internal hooks:
@@ -27,6 +28,7 @@ module MiGA::Dataset::Hooks
   def default_hooks
     {
       on_create: [[:recalculate_status]],
+      on_save: [[:check_type]],
       on_activate: [[:clear_run_counts], [:recalculate_status]],
       on_inactivate: [[:recalculate_status]],
       on_result_ready: [[:_pull_result_hooks]],
@@ -51,6 +53,12 @@ def hook_recalculate_status(_hook_args, _event_args)
     recalculate_status
   end
 
+  ##
+  # Ensure that the dataset type exists and is compatible with the project type
+  def hook_check_type(_hook_args, _event_args)
+    check_type
+  end
+
   ##
   # Run +cmd+ in the command-line with {{variables}}:
   # dataset, project, project_name, miga, object (if defined for the event)
diff --git a/lib/miga/dataset/result/ignore.rb b/lib/miga/dataset/result/ignore.rb
index 5b287dbd..9f0ad299 100644
--- a/lib/miga/dataset/result/ignore.rb
+++ b/lib/miga/dataset/result/ignore.rb
@@ -17,10 +17,14 @@ def ignore_task?(task)
   # - project: incompatible project
   # - noref: incompatible dataset, only for reference
   # - multi: incompatible dataset, only for multi
+  # - nomarkers: incompatible dataset, only for markers
   # - nonmulti: incompatible dataset, only for nonmulti
   # - complete: the task is already complete
   def ignore_reasons
-    %i[empty inactive upstream force project noref multi nonmulti complete]
+    %i[
+      empty inactive upstream force project
+      noref multi nonmulti nomarkers complete
+    ]
   end
 
   ##
@@ -91,9 +95,15 @@ def ignore_nonmulti?(task)
     ignore_by_type?(task, :nonmulti)
   end
 
+  ##
+  # Ignore +task+ because it's not a markers dataset
+  def ignore_nomarkers?(task)
+    ignore_by_type?(task, :nomarkers)
+  end
+
   ##
   # Ignore +task+ by +type+ of dataset, one of: +:noref+, +:multi+, or
-  # +:nonmulti+
+  # +:nonmulti+, +:nomarkers+
   def ignore_by_type?(task, type)
     return false if force_task?(task)
 
@@ -105,6 +115,8 @@ def ignore_by_type?(task, type)
         [:multi?, self.class.ONLY_MULTI_TASKS]
       when :nonmulti
         [:nonmulti?, self.class.ONLY_NONMULTI_TASKS]
+      when :nomarkers
+        [:markers?, self.class.EXCLUDE_NOMARKER_TASKS]
       else
         raise "Unexpected error, unknown type reason: #{type}"
       end
diff --git a/lib/miga/dataset/type.rb b/lib/miga/dataset/type.rb
new file mode 100644
index 00000000..358429b3
--- /dev/null
+++ b/lib/miga/dataset/type.rb
@@ -0,0 +1,51 @@
+##
+# Helper module including specific functions for dataset type
+module MiGA::Dataset::Type
+  ##
+  # Get the type of dataset as Symbol
+  def type
+    metadata[:type]
+  end
+
+  ##
+  # Is this dataset known to be multi-organism?
+  def multi?
+    self.class.KNOWN_TYPES.dig(type, :multi)
+  end
+
+  ##
+  # Is this dataset known to be single-organism?
+  def nonmulti?
+    y = self.class.KNOWN_TYPES.dig(type, :multi)
+    y.nil? ? nil : !y
+  end
+
+  ##
+  # Are universal marker genes expected to be found in this dataset?
+  def markers?
+    self.class.KNOWN_TYPES.dig(type, :markers)
+  end
+
+  ##
+  # Check that the dataset type is defined, known, and compatible with the
+  # project type and raise an exception if any of these checks fail
+  #
+  # If the dataset type is +:empty+, it returns +false+ without raising an
+  # exception, and true otherwise (and no tests are failed)
+  def check_type
+    raise MiGA::Error.new('Undefined dataset type') unless type
+    return false if type == :empty
+
+    unless self.class.KNOWN_TYPES[type]
+      raise MiGA::Error.new("Unknown dataset type: #{type}")
+    end
+    unless self.class.KNOWN_TYPES[type][:project_types].include? project.type
+      raise MiGA::Error.new(
+        "Dataset type (#{type}) incompatible with project (#{project.type})"
+      )
+    end
+
+    true
+  end
+
+end
diff --git a/lib/miga/json.rb b/lib/miga/json.rb
index 65ee306a..3e2735b4 100644
--- a/lib/miga/json.rb
+++ b/lib/miga/json.rb
@@ -69,5 +69,14 @@ def generate(obj, path = nil)
       File.open(path, 'w') { |fh| fh.print y } unless path.nil?
       y
     end
+
+    ##
+    # Generates and returns plain JSON to represent +obj+.
+    # If +path+ is passed, it saves the JSON in that file.
+    def generate_plain(obj, path = nil)
+      y = JSON.generate(obj)
+      File.open(path, 'w') { |fh| fh.print y } unless path.nil?
+      y
+    end
   end
 end
diff --git a/lib/miga/project.rb b/lib/miga/project.rb
index 02af6f6b..ad8ac211 100644
--- a/lib/miga/project.rb
+++ b/lib/miga/project.rb
@@ -98,7 +98,7 @@ def type
   ##
   # Is this a clade project?
   def clade?
-    type == :clade
+    %i[clade plasmids].include? type
   end
 
   ##
@@ -115,6 +115,12 @@ def multi?
   # Same as multi? For backward compatibility
   alias is_multi? multi?
 
+  ##
+  # Does the project support the use of universal markers?
+  def markers?
+    @@KNOWN_TYPES[type][:markers]
+  end
+
   ##
   # Is this project active? Currently a dummy function, returns
   # always true.
diff --git a/lib/miga/project/base.rb b/lib/miga/project/base.rb
index 5e046631..3dfcd5ad 100644
--- a/lib/miga/project/base.rb
+++ b/lib/miga/project/base.rb
@@ -89,32 +89,36 @@ module MiGA::Project::Base
   @@KNOWN_TYPES = {
     mixed: {
       description: 'Mixed collection of genomes, metagenomes, and viromes',
-      single: true, multi: true
+      single: true, multi: true, markers: true
     },
     genomes: {
       description: 'Collection of genomes',
-      single: true, multi: false
+      single: true, multi: false, markers: true
     },
     clade: {
       description: 'Collection of closely-related genomes (ANI >= 90%)',
-      single: true, multi: false
+      single: true, multi: false, markers: true
     },
     metagenomes: {
       description: 'Collection of metagenomes and/or viromes',
-      single: false, multi: true
+      single: false, multi: true, markers: true
+    },
+    plasmids: {
+      description: 'Collection of plasmids',
+      single: true, multi: false, markers: false
     }
   }
 
   ##
   # Project-wide distance estimations
-  @@DISTANCE_TASKS = [
-    :project_stats, :haai_distances, :aai_distances, :ani_distances,
-    :clade_finding
+  @@DISTANCE_TASKS = %i[
+    project_stats haai_distances aai_distances ani_distances
+    clade_finding
   ]
 
   ##
   # Project-wide tasks for :clade projects
-  @@INCLADE_TASKS = [:subclades, :ogs]
+  @@INCLADE_TASKS = %i[subclades ogs]
 
   ##
   # Options supported by projects
@@ -131,7 +135,9 @@ module MiGA::Project::Base
     },
     haai_p: {
       desc: 'Value of aai.rb -p on hAAI', type: String,
-      default: proc { |project| project.clade? ? 'no' : 'fastaai' },
+      default: proc { |project|
+        project.clade? || !project.markers? ? 'no' : 'fastaai'
+      },
       in: %w[blast+ blast blat diamond fastaai no]
     },
     aai_p: {
diff --git a/lib/miga/remote_dataset.rb b/lib/miga/remote_dataset.rb
index 0659867d..a58be34a 100644
--- a/lib/miga/remote_dataset.rb
+++ b/lib/miga/remote_dataset.rb
@@ -193,7 +193,7 @@ def get_gtdb_taxonomy
 
     doc = MiGA::Json.parse(
       MiGA::RemoteDataset.download(
-        :gtdb, :genome, gtdb_genome, 'taxon-history', nil, ['']
+        :gtdb, :genome, gtdb_genome, 'taxon-history'
       ),
       contents: true
     )
@@ -237,15 +237,24 @@ def ncbi_asm_json_doc
   private
 
   def get_ncbi_taxid_from_web
-    return nil if ncbi_asm_json_doc.nil?
+    # Check first if metadata was pulled from NCBI already
+    taxid = metadata.dig(:ncbi_dataset, :organism, :tax_id)
+    return taxid if taxid
 
-    ncbi_asm_json_doc['taxid']
+    # Otherwise, try to get the Assembly JSON document
+    ncbi_asm_json_doc&.dig('taxid')
   end
 
   def get_ncbi_taxid_from_ncbi
+    # Try first from Assembly data
     return get_ncbi_taxid_from_web if db == :assembly
 
-    doc = self.class.download(:ncbi, db, ids, :gb, nil, [], self).split(/\n/)
+    # Try from previously pulled NCBI data
+    taxid = metadata.dig(:ncbi_dataset, :organism, :tax_id)
+    return taxid if taxid
+
+    # Try from GenBank document (obtain it)
+    doc = self.class.download(:ncbi, db, ids, :gb, nil, {}, self).split(/\n/)
     ln = doc.grep(%r{^\s+/db_xref="taxon:}).first
     return nil if ln.nil?
 
@@ -283,14 +292,25 @@ def get_type_status_ncbi_nuccore(metadata)
   end
 
   def get_type_status_ncbi_asm(metadata)
-    return metadata if ncbi_asm_json_doc.nil?
+    from_type = nil
+
+    # Try first from previously pulled NCBI metadata
+    if metadata[:ncbi_dataset]
+      from_type = metadata.dig(
+        :ncbi_dataset, :type_material, :type_display_text
+      )
+    else
+      # Otherwise, check Assembly JSON document
+      return metadata if ncbi_asm_json_doc.nil?
+
+      metadata[:suspect] = (ncbi_asm_json_doc['exclfromrefseq'] || [])
+      metadata[:suspect] = nil if metadata[:suspect].empty?
+      return metadata if metadata[:is_type] # If predefined, as in SeqCode
 
-    metadata[:suspect] = (ncbi_asm_json_doc['exclfromrefseq'] || [])
-    metadata[:suspect] = nil if metadata[:suspect].empty?
-    return metadata if metadata[:is_type] # If predefined, as in SeqCode
+      from_type = ncbi_asm_json_doc['from_type']
+      from_type = ncbi_asm_json_doc['fromtype'] if from_type.nil?
+    end
 
-    from_type = ncbi_asm_json_doc['from_type']
-    from_type = ncbi_asm_json_doc['fromtype'] if from_type.nil?
     case from_type
     when nil
       # Do nothing
@@ -316,10 +336,11 @@ def save_assembly_to(project, name, udb)
     a_ctg = "#{base}.AllContigs.fna"
     File.open("#{base}.start", 'w') { |ofh| ofh.puts Time.now.to_s }
     if udb[:format] == :fasta_gz
-      download "#{l_ctg}.gz"
-      system "gzip -fd '#{l_ctg}.gz'"
+      l_ctg_gz = "#{l_ctg}.gz"
+      download(l_ctg_gz)
+      self.class.run_cmd(['gzip', '-f', '-d', l_ctg_gz])
     else
-      download l_ctg
+      download(l_ctg)
     end
     File.unlink(a_ctg) if File.exist? a_ctg
     File.open("#{base}.done", 'w') { |ofh| ofh.puts Time.now.to_s }
diff --git a/lib/miga/remote_dataset/base.rb b/lib/miga/remote_dataset/base.rb
index 3f4100e9..94918297 100644
--- a/lib/miga/remote_dataset/base.rb
+++ b/lib/miga/remote_dataset/base.rb
@@ -1,4 +1,3 @@
-require 'open-uri'
 require 'cgi'
 
 class MiGA::RemoteDataset < MiGA::MiGA
@@ -10,13 +9,24 @@ def UNIVERSE
   end
 end
 
+def uri_safe_join(*parts)
+  safe = parts.map { |i| i.is_a?(Array) ? i.join(',') : i.to_s }
+  last = safe.pop
+  safe.map! { |i| i[-1] == '/' ? i : "#{i}/" }
+  safe << last
+  URI::join(*safe)
+end
+
 module MiGA::RemoteDataset::Base
-  @@_EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
-  @@_EBI_API = 'https://www.ebi.ac.uk/Tools'
-  @@_GTDB_API = 'https://api.gtdb.ecogenomic.org'
-  @@_SEQCODE_API = 'https://disc-genomics.uibk.ac.at/seqcode'
-  @@_NCBI_API_KEY = lambda { |url|
-    ENV['NCBI_API_KEY'].nil? ? url : "#{url}&api_key=#{ENV['NCBI_API_KEY']}"
+  @@_NCBI_DATASETS = 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/'
+  @@_EUTILS        = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
+  @@_EBI_API       = 'https://www.ebi.ac.uk/Tools/'
+  @@_GTDB_API      = 'https://api.gtdb.ecogenomic.org/'
+  @@_SEQCODE_API   = 'https://disc-genomics.uibk.ac.at/seqcode/'
+  @@_EUTILS_BUILD  = lambda { |service, q|
+    q[:api_key] = ENV['NCBI_API_KEY'] if ENV['NCBI_API_KEY']
+    uri_safe_join(@@_EUTILS, "#{service}.fcgi")
+      .tap { |uri| uri.query = URI.encode_www_form(q) }
   }
 
   ##
@@ -25,15 +35,13 @@ module MiGA::RemoteDataset::Base
   # supported keys as Symbol:
   # - +:dbs+ => Hash with keys being the database name and the values a Hash of
   #   properties such as +stage+, +format+, +map_to+, and +getter+.
-  # - +url+ => Pattern of the URL where the data can be obtained, where +%1$s+
-  #   is the name of the database, +%2$s+ is the IDs, and +%3$s+ is format.
-  #   Additional parameters can be passed to certain functions using the +extra+
-  #   option.
+  # - +uri+ => Function producing a parsed URI object, accepting one parameter:
+  #   a Hash of options.
   # - +method+ => Method used to query the URL. Only +:rest+ and +:net+ are
   #   currently supported.
-  # - +api_key+ => A lambda function that takes a URL as input and returns the
-  #   URL to be downloaded with an API Key (if available).
   # - +map_to_universe+ => Universe where results map to. Currently unsupported.
+  # - +scheme+ => Function returning the scheme used as a String (ftp, http,
+  #   https). Mandatory if method is :net.
   @@UNIVERSE = {
     web: {
       dbs: {
@@ -41,13 +49,18 @@ module MiGA::RemoteDataset::Base
         assembly_gz: { stage: :assembly, format: :fasta_gz },
         text: { stage: :metadata, format: :text }
       },
-      url: '%2$s',
+      uri: lambda { |opts| URI.parse(opts[:ids][0]) },
+      scheme: lambda { |opts| opts[:ids][0].split(':', 2)[0] },
       method: :net
     },
     ebi: {
       dbs: { embl: { stage: :assembly, format: :fasta } },
-      url: "#{@@_EBI_API}/dbfetch/dbfetch/%1$s/%2$s/%3$s",
-      method: :rest
+      uri: lambda do |opts|
+        uri_safe_join(
+          @@_EBI_API, 'dbfetch', 'dbfetch', opts[:db], opts[:ids], opts[:format]
+        )
+      end,
+      method: :get
     },
     gtdb: {
       dbs: {
@@ -56,15 +69,18 @@ module MiGA::RemoteDataset::Base
         # The 'taxon' namespace actually returns a list of genomes (+format+)
         taxon: {
           stage: :metadata, format: :genomes, map_to: [:assembly],
-          extra: ['sp_reps_only=false']
+          extra: { sp_reps_only: false }
         },
         # The 'genome' namespace actually returns the taxonomy (+format+)
         genome: { stage: :metadata, format: 'taxon-history' }
       },
-      url: "#{@@_GTDB_API}/%1$s/%2$s/%3$s?%4$s",
-      method: :rest,
+      uri: lambda do |opts|
+        uri_safe_join(@@_GTDB_API, opts[:db], opts[:ids], opts[:format])
+          .tap { |uri| uri.query = URI.encode_www_form(opts[:extra]) }
+      end,
+      method: :get,
       map_to_universe: :ncbi,
-      headers: 'accept: application/json' # < TODO not currently supported
+      headers: lambda { |_opts| { 'Accept' => 'application/json' } }
     },
     seqcode: {
       dbs: {
@@ -74,8 +90,11 @@ module MiGA::RemoteDataset::Base
         # This is the list of type genomes
         :'type-genomes' => { stage: :metadata, format: :json }
       },
-      url: "#{@@_SEQCODE_API}/%1$s.json?%4$s",
-      method: :rest,
+      uri: lambda do |opts|
+        uri_safe_join(@@_SEQCODE_API, "#{opts[:db]}.json")
+          .tap { |uri| uri.query = URI.encode_www_form(opts[:extra]) }
+      end,
+      method: :get,
       map_to_universe: :ncbi
     },
     ncbi: {
@@ -84,9 +103,12 @@ module MiGA::RemoteDataset::Base
         assembly: { stage: :assembly, format: :fasta_gz, getter: :ncbi_asm },
         taxonomy: { stage: :metadata, format: :xml }
       },
-      url: "#{@@_EUTILS}efetch.fcgi?db=%1$s&id=%2$s&rettype=%3$s&retmode=text",
-      method: :rest,
-      api_key: @@_NCBI_API_KEY
+      uri: lambda do |opts|
+        @@_EUTILS_BUILD[:efetch,
+          db: opts[:db], id: opts[:ids], rettype: opts[:format], retmode: :text
+        ]
+      end,
+      method: :get
     },
     ncbi_map: {
       dbs: {
@@ -95,22 +117,81 @@ module MiGA::RemoteDataset::Base
         },
         biosample: { stage: :metadata, map_to: [:assembly], format: :json }
       },
-      url: "#{@@_EUTILS}elink.fcgi?dbfrom=%1$s&id=%2$s&db=%4$s&retmode=%3$s",
-      method: :net,
-      map_to_universe: :ncbi,
-      api_key: @@_NCBI_API_KEY
+      uri: lambda do |opts|
+        @@_EUTILS_BUILD[:elink, {
+          dbfrom: opts[:db], id: opts[:ids], retmode: opts[:format]
+        }.merge(opts[:extra])]
+      end,
+      method: :get,
+      map_to_universe: :ncbi
     },
     ncbi_summary: {
       dbs: { assembly: { stage: :metadata, format: :json } },
-      url: "#{@@_EUTILS}esummary.fcgi?db=%1$s&id=%2$s&retmode=%3$s",
-      method: :rest,
-      api_key: @@_NCBI_API_KEY
+      uri: lambda do |opts|
+        @@_EUTILS_BUILD[:esummary,
+          db: opts[:db], id: opts[:ids], retmode: opts[:format]
+        ]
+      end,
+      method: :get
     },
     ncbi_search: {
-      dbs: { assembly: { stage: :metadata, format: :json } },
-      url: "#{@@_EUTILS}esearch.fcgi?db=%1$s&term=%2$s&retmode=%3$s",
-      method: :rest,
-      api_key: @@_NCBI_API_KEY
+      dbs: {
+        assembly: { stage: :metadata, format: :json },
+        taxonomy: { stage: :metadata, format: :json }
+      },
+      uri: lambda do |opts|
+        @@_EUTILS_BUILD[:esearch,
+          db: opts[:db], term: opts[:ids], retmode: opts[:format]
+        ]
+      end,
+      method: :get
+    },
+    ncbi_datasets_download: {
+      dbs: { genome: { stage: :assembly, format: :zip } },
+      uri: lambda do |opts|
+        q = { include_annotation_type: 'GENOME_FASTA' }
+        uri_safe_join(
+          @@_NCBI_DATASETS, opts[:db], :accession, opts[:ids], :download
+        ).tap { |uri| uri.query = URI.encode_www_form(q) }
+      end,
+      method: :get,
+      headers: lambda do |opts|
+        {}.tap do |h|
+          h['Accept'] = 'application/zip' if opts[:format] == :zip
+          h['api-key'] = ENV['NCBI_API_KEY'] if ENV['NCBI_API_KEY']
+        end
+      end
+    },
+    ncbi_datasets: {
+      dbs: {
+        genome: {
+          stage: :metadata, format: :json, extra: { action: 'dataset_report' }
+        }
+      },
+      uri: lambda do |opts|
+        uri_safe_join(@@_NCBI_DATASETS, opts[:db], opts[:extra][:action])
+      end,
+      payload: lambda do |opts|
+        query = opts[:ids][0]
+        q = {
+          filters: {
+            assembly_version: 'current',
+            exclude_paired_reports: true
+          }.merge(query[:filters] || {}),
+          page_size: query[:page_size] || 1_000,
+          returned_content: 'COMPLETE'
+        }
+        q[:page_token] = query[:page_token] if query[:page_token]
+        q[:taxons] = query[:taxons] if query[:taxons]
+        MiGA::Json.generate_plain(q)
+      end,
+      headers: lambda do |opts|
+        {}.tap do |h|
+          h['api-key'] = ENV['NCBI_API_KEY'] if ENV['NCBI_API_KEY']
+          h['Content-Type'] = 'application/json' if opts[:format] == :json
+        end
+      end,
+      method: :post
     }
   }
 end
diff --git a/lib/miga/remote_dataset/download.rb b/lib/miga/remote_dataset/download.rb
index 48548025..c635c273 100644
--- a/lib/miga/remote_dataset/download.rb
+++ b/lib/miga/remote_dataset/download.rb
@@ -6,28 +6,40 @@ class MiGA::RemoteDataset
   # Class-level
   class << self
     ##
-    # Download data from the +universe+ in the database +db+ with IDs +ids+ and
-    # in +format+. If passed, it saves the result in +file+. Additional
-    # parameters specific to the download method can be passed using +extra+.
-    # Returns String. The +obj+ can also be passed as MiGA::RemoteDataset or
-    # MiGA::Dataset.
-    def download(universe, db, ids, format, file = nil, extra = [], obj = nil)
-      ids = [ids] unless ids.is_a? Array
-      getter = @@UNIVERSE[universe][:dbs][db][:getter] || :download
-      method = @@UNIVERSE[universe][:method]
-      opts = {
-        universe: universe,
-        db: db,
-        ids: ids,
-        format: format,
-        file: file,
-        extra: extra,
-        obj: obj
+    # Return hash of options used internally for the getter methods, including
+    # by +download+. The prepared request is for data from the +universe+ in the
+    # database +db+ with IDs +ids+ and in +format+. If passed, it saves the
+    # result in +file+. Additional parameters specific to the download method
+    # can be passed using +extra+. The +obj+ can also be passed as
+    # MiGA::RemoteDataset or MiGA::Dataset
+    def download_opts(
+          universe, db, ids, format, file = nil, extra = {}, obj = nil)
+      universe_hash = @@UNIVERSE[universe]
+      database_hash = universe_hash.dig(:dbs, db)
+      getter = database_hash[:getter] || :download
+      action = database_hash[:method] || universe_hash[:method]
+
+      {
+        universe: universe,  db:   db,    ids: ids.is_a?(Array) ? ids : [ids],
+        format:   format,    file: file,  obj: obj,
+        extra:    (database_hash[:extra] || {}).merge(extra),
+        _fun:     :"#{getter}_#{action}"
       }
-      doc = send("#{getter}_#{method}", opts)
+    end
+
+    ##
+    # Returns String. The prequired parameters (+params+) are identical to those
+    # of +download_opts+ (see for details)
+    def download(*params)
+      opts = download_opts(*params)
+      doc = send(opts[:_fun], opts)
+
       unless opts[:file].nil?
         ofh = File.open(opts[:file], 'w')
-        ofh.print doc.force_encoding('UTF-8')
+        unless opts[:file] =~ /\.([gb]?z|tar|zip|rar)$/i
+          doc = normalize_encoding(doc)
+        end
+        ofh.print doc
         ofh.close
       end
       doc
@@ -39,9 +51,9 @@ def download(universe, db, ids, format, file = nil, extra = [], obj = nil)
     # +obj+ (mandatory): MiGA::RemoteDataset
     # +ids+ (mandatory): String or Array of String
     # +file+: String, passed to download
-    # +extra+: Array, passed to download
+    # +extra+: Hash, passed to download
     # +format+: String, passed to download
-    def ncbi_asm_rest(opts)
+    def ncbi_asm_get(opts)
       url_dir = opts[:obj].ncbi_asm_json_doc&.dig('ftppath_genbank')
       if url_dir.nil? || url_dir.empty?
         raise MiGA::RemoteDataMissingError.new(
@@ -58,8 +70,8 @@ def ncbi_asm_rest(opts)
 
     ##
     # Download data from NCBI GenBank (nuccore) database using the REST method.
-    # Supported +opts+ (Hash) are the same as #download_rest and #ncbi_asm_rest.
-    def ncbi_gb_rest(opts)
+    # Supported +opts+ (Hash) are the same as #download_rest and #ncbi_asm_get.
+    def ncbi_gb_get(opts)
       # Simply use defaults, but ensure that the URL can be properly formed
       o = download_rest(opts.merge(universe: :ncbi, db: :nuccore))
       return o unless o.strip.empty?
@@ -70,54 +82,83 @@ def ncbi_gb_rest(opts)
         File.unlink(opts[:file]) if File.exist? opts[:file]
         opts[:file] = "#{opts[:file]}.gz"
       end
-      ncbi_asm_rest(opts)
+      ncbi_asm_get(opts)
     end
 
     ##
-    # Download data using the REST method. Supported +opts+ (Hash) include:
+    # Download data using the GET method. Supported +opts+ (Hash) include:
     # +universe+ (mandatory): Symbol
-    # +db+ (mandatory): Symbol
-    # +ids+ (mandatory): Array of String
+    # +db+: Symbol
+    # +ids+: Array of String
     # +format+: String
-    # +extra+: Array
-    def download_rest(opts)
+    # +extra+: Hash
+    def download_get(opts)
       u = @@UNIVERSE[opts[:universe]]
-      url = sprintf(
-        u[:url], opts[:db], opts[:ids].join(','), opts[:format], *opts[:extra]
-      )
-      url = u[:api_key][url] unless u[:api_key].nil?
-      download_url url
+      download_uri(u[:uri][opts], u[:headers] ? u[:headers][opts] : {})
+    end
+
+    ##
+    # Download data using the POST method. Supported +opts+ (Hash) include:
+    # +universe+ (mandatory): Symbol
+    # +db+: Symbol
+    # +ids+: Array of String
+    # +format+: String
+    # +extra+: Hash
+    def download_post(opts)
+      u = @@UNIVERSE[opts[:universe]]
+      uri = u[:uri][opts]
+      payload = u[:payload] ? u[:payload][opts] : ''
+      headers = u[:headers] ? u[:headers][opts] : {}
+      net_method(:post, uri, payload, headers)
+    end
+
+    ##
+    # Download data using the FTP protocol. Supported +opts+ (Hash) include:
+    # +universe+ (mandatory): Symbol
+    # +db+: Symbol
+    # +ids+: Array of String
+    # +format+: String
+    # +extra+: Hash
+    def download_ftp(opts)
+      u = @@UNIVERSE[opts[:universe]]
+      net_method(:ftp, u[:uri][opts])
+    end
+
+    ##
+    # Redirects to +download_get+ or +download_ftp+, depending on the URI's
+    # protocol
+    def download_net(opts)
+      u = @@UNIVERSE[opts[:universe]]
+      if u[:scheme][opts] == 'ftp'
+        download_ftp(opts)
+      else
+        download_get(opts)
+      end
     end
 
     ##
     # Alias of download_rest
-    alias download_net download_rest
+    alias download_rest download_get
+
+    ##
+    # Download the given +URI+ and return the result regardless of response
+    # code. Attempts download up to three times before raising Net::ReadTimeout.
+    def download_uri(uri, headers = {})
+      net_method(:get, uri, headers)
+    end
 
     ##
     # Download the given +url+ and return the result regardless of response
     # code. Attempts download up to three times before raising Net::ReadTimeout.
-    def download_url(url)
-      doc = ''
-      @timeout_try = 0
-      begin
-        DEBUG 'GET: ' + url
-        URI.parse(url).open(read_timeout: 600) { |f| doc = f.read }
-      rescue => e
-        @timeout_try += 1
-        raise e if @timeout_try >= 3
-
-        sleep 5 # <- For: 429 Too Many Requests
-        DEBUG "RETRYING after: #{e}"
-        retry
-      end
-      doc
+    def download_url(url, headers = {})
+      download_uri(URI.parse(url), headers)
     end
 
     ##
     # Looks for the entry +id+ in +dbfrom+, and returns the linked
     # identifier in +db+ (or nil).
     def ncbi_map(id, dbfrom, db)
-      doc = download(:ncbi_map, dbfrom, id, :json, nil, [db])
+      doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
       return if doc.empty?
 
       tree = MiGA::Json.parse(doc, contents: true)
@@ -134,8 +175,34 @@ module MiGA::RemoteDataset::Download
   ##
   # Download data into +file+
   def download(file)
-    format = self.class.UNIVERSE[universe][:dbs][db][:format]
-    # MiGA::MiGA.DEBUG "download: #{universe}, #{db}, #{ids}, #{format}"
-    self.class.download(universe, db, ids, format, file, [], self)
+    self.class.download(*download_params(file))
+  end
+
+  def universe_hash
+    self.class.UNIVERSE[universe]
+  end
+
+  def database_hash
+    universe_hash.dig(:dbs, db)
+  end
+
+  def download_params(file = nil)
+    [universe, db, ids, database_hash[:format], file, {}, self]
+  end
+
+  def download_opts(file = nil)
+    self.class.download_opts(*download_params(file))
+  end
+
+  def download_uri
+    universe_hash[:uri][download_opts]
+  end
+
+  def download_headers
+    universe_hash[:headers][download_opts]
+  end
+
+  def download_payload
+    universe_hash[:payload][download_opts]
   end
 end
diff --git a/lib/miga/result.rb b/lib/miga/result.rb
index f661095e..2d9cd454 100644
--- a/lib/miga/result.rb
+++ b/lib/miga/result.rb
@@ -3,6 +3,7 @@
 require 'miga/result/dates'
 require 'miga/result/source'
 require 'miga/result/stats'
+require 'miga/result/versions'
 
 ##
 # The result from a task run. It can be project-wide or dataset-specific.
@@ -10,6 +11,7 @@ class MiGA::Result < MiGA::MiGA
   include MiGA::Result::Dates
   include MiGA::Result::Source
   include MiGA::Result::Stats
+  include MiGA::Result::Versions
 
   # Class-level
   class << self
@@ -151,7 +153,11 @@ def add_files(files)
   ##
   # Initialize and #save empty result
   def create
-    @data = { created: Time.now.to_s, stats: {}, files: {} }
+    @data = {
+      created: Time.now.to_s,
+      stats: {}, files: {},
+      versions: { 'MiGA' => MiGA::VERSION.join('.') }
+    }
     save
   end
 
diff --git a/lib/miga/result/versions.rb b/lib/miga/result/versions.rb
new file mode 100644
index 00000000..ea8aeb06
--- /dev/null
+++ b/lib/miga/result/versions.rb
@@ -0,0 +1,23 @@
+require 'miga/result/base'
+
+##
+# Helper module including functions for results to handle software versions
+module MiGA::Result::Versions
+  ##
+  # Return the versions hash
+  def versions
+    self[:versions]
+  end
+
+  ##
+  # Add version information for the Software used by this result
+  def add_versions(versions)
+    versions.each { |k, v| self[:versions][k.to_sym] = v }
+  end
+
+  ##
+  # Get list of software and their versions as raw text (Markdown)
+  def versions_md
+    versions.map { |k, v| "- #{k}: #{v}" }.join("\n")
+  end
+end
diff --git a/lib/miga/taxonomy/base.rb b/lib/miga/taxonomy/base.rb
index d524132a..fd5806e8 100644
--- a/lib/miga/taxonomy/base.rb
+++ b/lib/miga/taxonomy/base.rb
@@ -6,14 +6,15 @@ class << self
     ##
     # Returns cannonical rank (Symbol) for the +rank+ String
     def normalize_rank(rank)
+      return unless rank
       return rank.to_sym if @@_KNOWN_RANKS_H[rank.to_sym]
 
       rank = rank.to_s.downcase
-      return nil if rank == 'no rank'
+      return if rank == 'no rank'
 
       rank = @@RANK_SYNONYMS[rank] unless @@RANK_SYNONYMS[rank].nil?
       rank = rank.to_sym
-      return nil unless @@_KNOWN_RANKS_H[rank]
+      return unless @@_KNOWN_RANKS_H[rank]
 
       rank
     end
diff --git a/lib/miga/version.rb b/lib/miga/version.rb
index 9a54a8cf..60a1d903 100644
--- a/lib/miga/version.rb
+++ b/lib/miga/version.rb
@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 8, 3].freeze
+  VERSION = [1.3, 9, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 10, 10)
+  VERSION_DATE = Date.new(2024, 1, 22)
 
   ##
   # References of MiGA
diff --git a/scripts/assembly.bash b/scripts/assembly.bash
index ffe6b095..ad66ae66 100755
--- a/scripts/assembly.bash
+++ b/scripts/assembly.bash
@@ -10,6 +10,7 @@ cd "$PROJECT/data/05.assembly"
 miga date > "$DATASET.start"
 
 # Interpose (if needed)
+interpose=no
 TF="../04.trimmed_fasta"
 b=$DATASET
 if [[ -s "$TF/${b}.2.fasta" || -s "$TF/${b}.2.fasta.gz" ]] ; then
@@ -22,6 +23,7 @@ if [[ -s "$TF/${b}.2.fasta" || -s "$TF/${b}.2.fasta.gz" ]] ; then
         gzip -cd "$TF/${b}.${s}.fasta.gz" > "${b}.${s}.tmp"
       fi
     done
+    interpose=yes
     FastA.interpose.pl "$cr" "$b".[12].tmp
     rm "$b".[12].tmp
     miga add_result -P "$PROJECT" -D "$DATASET" -r trimmed_fasta -f
@@ -62,5 +64,17 @@ FastA.length.pl "$DATASET.AllContigs.fna" | awk '$2>=1000{print $1}' \
 
 # Finalize
 miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$interpose" == "yes" ]] ; then
+    echo "=> Enveomics Collection: FastA.interpose.pl"
+    echo "version unknown"
+  fi
+)
+=> IDBA-UD
+version unknown
+VERSIONS
 
diff --git a/scripts/cds.bash b/scripts/cds.bash
index 5db4ba39..35ca5b6d 100755
--- a/scripts/cds.bash
+++ b/scripts/cds.bash
@@ -19,7 +19,7 @@ fi
 # Run Prodigal
 TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
 case "$TYPE" in
-  metagenome|virome)
+  metagenome|virome|plasmid)
     prodigal -a "${DATASET}.faa" -d "${DATASET}.fna" -o "${DATASET}.gff3" \
       -f gff -q -i "../05.assembly/${DATASET}.LargeContigs.fna" -p meta
     ;;
@@ -68,6 +68,12 @@ for ext in gff3 faa fna ; do
 done
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+=> Prodigal
+$(prodigal -v 2>&1 | grep . | perl -pe 's/^Prodigal //')
+VERSIONS
 
diff --git a/scripts/distances.bash b/scripts/distances.bash
index e665e62e..7b3feb77 100755
--- a/scripts/distances.bash
+++ b/scripts/distances.bash
@@ -10,13 +10,111 @@ cd "$PROJECT/data/09.distances"
 miga date > "$DATASET.start"
 
 # Check quality
-miga stats -P "$PROJECT" -D "$DATASET" -r essential_genes --compute-and-save
-inactive=$(miga ls -P "$PROJECT" -D "$DATASET" -m inactive | cut -f 2)
-[[ "$inactive" == "true" ]] && exit
+MARKERS=$(miga ls -P "$PROJECT" -D "$DATASET" --markers \
+  | wc -l | awk '{print $1}')
+if [[ "$MARKERS" -eq "1" ]] ; then
+  miga stats -P "$PROJECT" -D "$DATASET" -r essential_genes --compute-and-save
+  inactive=$(miga ls -P "$PROJECT" -D "$DATASET" -m inactive | cut -f 2)
+  [[ "$inactive" == "true" ]] && exit
+fi
 
 # Run distances
 ruby -I "$MIGA/lib" "$MIGA/utils/distances.rb" "$PROJECT" "$DATASET"
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+fastaai=no
+aai=no
+ani=no
+blast=no
+blat=no
+diamond=no
+fastani=no
+case $(miga option -P "$PROJECT" -k haai_p) in
+  fastaai)
+    fastaai=yes
+    ;;
+  diamond)
+    diamond=yes
+    aai=yes
+    ;;
+  blast)
+    blast=yes
+    aai=yes
+    ;;
+esac
+
+case $(miga option -P "$PROJECT" -k aai_p) in
+  diamond)
+    diamond=yes
+    aai=yes
+    ;;
+  blast)
+    blast=yes
+    aai=yes
+    ;;
+esac
+
+case $(miga option -P "$PROJECT" -k ani_p) in
+  blast)
+    blast=yes
+    ani=yes
+    ;;
+  blat)
+    blat=yes
+    ani=yes
+    ;;
+  fastani)
+    fastani=yes
+    ;;
+esac
+
+
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$fastaai" == "yes" ]] ; then
+    echo "=> FastAAI"
+    fastaai version 2>&1 | perl -pe 's/.*=//'
+  fi
+)
+$(
+  if [[ "$fastani" == "yes" ]] ; then
+    echo "=> FastANI"
+    fastANI --version 2>&1 | grep . | perl -pe 's/^version //'
+  fi
+)
+$(
+  if [[ "$aai" == "yes" ]] ; then
+    echo "=> Enveomics Collection: aai.rb"
+    aai.rb --version 2>&1 | perl -pe 's/.*: //'
+  fi
+)
+$(
+  if [[ "$ani" == "yes" ]] ; then
+    echo "=> Enveomics Collection: ani.rb"
+    ani.rb --version 2>&1 | perl -pe 's/.*: //'
+  fi
+)
+$(
+  if [[ "$blast" == "yes" ]] ; then
+    echo "=> NCBI BLAST+"
+    blastp -version 2>&1 | tail -n 1 | perl -pe 's/.*: blast //'
+  fi
+)
+$(
+  if [[ "$blat" == "yes" ]] ; then
+    echo "=> BLAT"
+    blat 2>&1 | head -n 1 | perl -pe 's/.* v\. //' | perl -pe 's/ fast .*//'
+  fi
+)
+$(
+  if [[ "$diamond" == "yes" ]] ; then
+    echo "=> Diamond"
+    diamond --version 2>&1 | perl -pe 's/^diamond version //'
+  fi
+)
+VERSIONS
+
diff --git a/scripts/essential_genes.bash b/scripts/essential_genes.bash
index 6e36f9e2..a5bb97ea 100755
--- a/scripts/essential_genes.bash
+++ b/scripts/essential_genes.bash
@@ -70,4 +70,17 @@ fi
 
 # Finalize
 miga date > "${DATASET}.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+=> Enveomics Collection: HMM.essential.rb
+$(HMM.essential.rb --version 2>&1 | perl -pe 's/.*: //')
+$(
+  if [[ "$NOMULTI" -eq "1" ]] ; then
+    echo "=> FastAAI"
+    fastaai version 2>&1 | perl -pe 's/.*=//'
+  fi
+)
+VERSIONS
+
diff --git a/scripts/mytaxa.bash b/scripts/mytaxa.bash
index d6ff4260..10c10485 100755
--- a/scripts/mytaxa.bash
+++ b/scripts/mytaxa.bash
@@ -15,7 +15,7 @@ if [[ "$MIGA_MYTAXA" == "no" ]] ; then
     > "$DATASET.nomytaxa.txt"
 else
   # Check type of dataset
-  MULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --multi \
+  MULTI=$(miga ls -P "$PROJECT" -D "$DATASET" --multi \
     | wc -l | awk '{print $1}')
   if [[ "$MULTI" -eq "1" ]] ; then
     # Check requirements
@@ -98,5 +98,20 @@ else
 fi
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$MIGA_MYTAXA" != "no" && "$MULTI" -eq "1" ]] ; then
+    echo "=> MyTaxa"
+    MyTaxa | grep Version: | perl -pe 's/.*: //'
+    echo "=> Diamond"
+    diamond --version 2>&1 | perl -pe 's/^diamond version //'
+    echo "=> Krona"
+    ktImportText | head -n 2 | tail -n 1 | awk '{ print $3 }'
+  fi
+)
+VERSIONS
+
diff --git a/scripts/mytaxa_scan.bash b/scripts/mytaxa_scan.bash
index 4a64db27..41dcee0c 100755
--- a/scripts/mytaxa_scan.bash
+++ b/scripts/mytaxa_scan.bash
@@ -14,7 +14,7 @@ if [[ "$MIGA_MYTAXA" == "no" ]] ; then
     > "$DATASET.nomytaxa.txt"
 else
   # Check type of dataset
-  NOMULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --no-multi \
+  NOMULTI=$(miga ls -P "$PROJECT" -D "$DATASET" --no-multi \
     | wc -l | awk '{print $1}')
   if [[ "$NOMULTI" -eq "1" ]] ; then
     # Check requirements
@@ -97,5 +97,18 @@ else
 fi
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$MIGA_MYTAXA" != "no" && "$NOMULTI" -eq "1" ]] ; then
+    echo "=> MyTaxa"
+    MyTaxa | grep Version: | perl -pe 's/.*: //'
+    echo "=> Diamond"
+    diamond --version 2>&1 | perl -pe 's/^diamond version //'
+  fi
+)
+VERSIONS
+
diff --git a/scripts/read_quality.bash b/scripts/read_quality.bash
index 2adfc225..7021d5f8 100755
--- a/scripts/read_quality.bash
+++ b/scripts/read_quality.bash
@@ -19,6 +19,10 @@ for s in 1 2 ; do
 done
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+VERSIONS
 
diff --git a/scripts/ssu.bash b/scripts/ssu.bash
index 6ae2abbd..f130b0ae 100755
--- a/scripts/ssu.bash
+++ b/scripts/ssu.bash
@@ -65,4 +65,22 @@ fi
 
 # Finalize
 miga date > "${DATASET}.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ -s $fa ]] ; then
+    echo "=> barrnap"
+    barrnap --version 2>&1 | perl -pe 's/^barrnap //'
+    echo "=> bedtools"
+    bedtools --version 2>&1 | perl -pe 's/^bedtools //'
+    echo "=> Enveomics Collection"
+    echo "version unknown"
+    echo "=> RDP Naive Bayes Classifier"
+    gzip -cd "${DATASET}.rdp.tsv.gz" | tail -n 1 | perl -pe 's/.*: //'
+    echo "=> tRNAscan-SE"
+    tRNAscan-SE -h 2>&1 | head -n 2 | tail -n 1 | perl -pe 's/^tRNAscan-SE //'
+  fi
+)
+VERSIONS
diff --git a/scripts/stats.bash b/scripts/stats.bash
index 8d5a2c70..b3c37ace 100755
--- a/scripts/stats.bash
+++ b/scripts/stats.bash
@@ -12,11 +12,17 @@ cd "$DIR"
 miga date > "${DATASET}.start"
 
 # Calculate statistics
-for i in raw_reads trimmed_fasta assembly cds essential_genes distances taxonomy ssu ; do
+for i in raw_reads trimmed_fasta assembly \
+         cds essential_genes distances taxonomy ssu ; do
   echo "# $i"
   miga stats --compute-and-save --ignore-empty -P "$PROJECT" -D "$DATASET" -r $i
 done
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+VERSIONS
+
diff --git a/scripts/taxonomy.bash b/scripts/taxonomy.bash
index 25bb8cf1..637a882e 100755
--- a/scripts/taxonomy.bash
+++ b/scripts/taxonomy.bash
@@ -16,5 +16,101 @@ ruby -I "$MIGA/lib" \
       "$MIGA/utils/distances.rb" "$PROJECT" "$DATASET" run_taxonomy=1
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+fastaai=no
+aai=no
+ani=no
+blast=no
+blat=no
+diamond=no
+fastani=no
+REF_PROJECT=$(miga option -P "$PROJECT" -k ref_project)
+if [[ -S "$REF_PROJECT" ]] ; then
+  case $(miga option -P "$REF_PROJECT" -k haai_p) in
+    fastaai)
+      fastaai=yes
+      ;;
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
+
+  case $(miga option -P "$REF_PROJECT" -k aai_p) in
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
+
+  case $(miga option -P "$REF_PROJECT" -k ani_p) in
+    blast)
+      blast=yes
+      ani=yes
+      ;;
+    blat)
+      blat=yes
+      ani=yes
+    ;;
+  fastani)
+    fastani=yes
+    ;;
+  esac
+fi
+
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$fastaai" == "yes" ]] ; then
+    echo "=> FastAAI"
+    fastaai version 2>&1 | perl -pe 's/.*=//'
+  fi
+)
+$(
+  if [[ "$fastani" == "yes" ]] ; then
+    echo "=> FastANI"
+    fastANI --version 2>&1 | grep . | perl -pe 's/^version //'
+  fi
+)
+$(
+  if [[ "$aai" == "yes" ]] ; then
+    echo "=> Enveomics Collection: aai.rb"
+    aai.rb --version 2>&1 | perl -pe 's/.*: //'
+  fi
+)
+$(
+  if [[ "$ani" == "yes" ]] ; then
+    echo "=> Enveomics Collection: ani.rb"
+    ani.rb --version 2>&1 | perl -pe 's/.*: //'
+  fi
+)
+$(
+  if [[ "$blast" == "yes" ]] ; then
+    echo "=> NCBI BLAST+"
+    blastp -version 2>&1 | tail -n 1 | perl -pe 's/.*: blast //'
+  fi
+)
+$(
+  if [[ "$blat" == "yes" ]] ; then
+    echo "=> BLAT"
+    blat 2>&1 | head -n 1 | perl -pe 's/.* v\. //' | perl -pe 's/ fast .*//'
+  fi
+)
+$(
+  if [[ "$diamond" == "yes" ]] ; then
+    echo "=> Diamond"
+    diamond --version 2>&1 | perl -pe 's/^diamond version //'
+  fi
+)
+VERSIONS
+
diff --git a/scripts/trimmed_fasta.bash b/scripts/trimmed_fasta.bash
index 978b1da5..4824b6b8 100755
--- a/scripts/trimmed_fasta.bash
+++ b/scripts/trimmed_fasta.bash
@@ -32,6 +32,14 @@ for x in 1.fasta 2.fasta SingleReads.fa CoupledReads.fa ; do
 done
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+=> Enveomics Collection: FastQ.maskQual.rb
+$(FastQ.maskQual.rb --version | perl -pe 's/.* //')
+=> Enveomics Collection: FastA.interpose.pl
+version unknown
+VERSIONS
 
diff --git a/scripts/trimmed_reads.bash b/scripts/trimmed_reads.bash
index 30fb508f..ef901524 100755
--- a/scripts/trimmed_reads.bash
+++ b/scripts/trimmed_reads.bash
@@ -36,15 +36,19 @@ if [[ -s "$b.2.fastq.gz" ]] ; then
   $CMD -1 "$b.1.fastq.gz" -2 "$b.2.fastq.gz"
   for s in 1 2 ; do
     mv "$b/${s}.post_trim_${b}.${s}.fq.gz" "${b}.${s}.clipped.fastq.gz"
-    mv "$b/${s}.pre_trim_QC_${b}.${s}.html" "../03.read_quality/${b}.pre.${s}.html"
-    mv "$b/${s}.post_trim_QC_${b}.${s}.html" "../03.read_quality/${b}.post.${s}.html"
+    mv "$b/${s}.pre_trim_QC_${b}.${s}.html" \
+       "../03.read_quality/${b}.pre.${s}.html"
+    mv "$b/${s}.post_trim_QC_${b}.${s}.html" \
+       "../03.read_quality/${b}.post.${s}.html"
   done
 else
   # Unpaired
   $CMD -u "$b.1.fastq.gz"
   mv "$b/unpaired.post_trim_${b}.1.fq.gz" "${b}.1.clipped.fastq.gz"
-  mv "$b/unpaired.pre_trim_QC_${b}.1.html" "../03.read_quality/${b}.pre.1.html"
-  mv "$b/unpaired.post_trim_QC_${b}.1.html" "../03.read_quality/${b}.post.1.html"
+  mv "$b/unpaired.pre_trim_QC_${b}.1.html" \
+     "../03.read_quality/${b}.pre.1.html"
+  mv "$b/unpaired.post_trim_QC_${b}.1.html" \
+     "../03.read_quality/${b}.post.1.html"
 fi
 mv "$b/Subsample_Adapter_Detection.stats.txt" \
   "../03.read_quality/$b.adapters.txt"
@@ -54,6 +58,22 @@ rm -r "$b"
 rm -f "$b".[12].fastq.gz
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+=> Enveomics Collection: FastQ.tag.rb
+$(FastQ.tag.rb --version | perl -pe 's/.* //')
+=> Multitrim
+version unknown
+=> FaQCs
+$(FaQCs --version 2>&1 | perl -pe 's/.*: //')
+=> Seqtk
+$(seqtk 2>&1 | grep Version | perl -pe 's/.*: //')
+=> Fastp
+$(fastp --version 2>&1 | perl -pe 's/^fastp //')
+=> Falco
+$(falco -V 2>&1 | tee)
+VERSIONS
 
diff --git a/test/dataset_test.rb b/test/dataset_test.rb
index 2a4baa91..52b7ce50 100644
--- a/test/dataset_test.rb
+++ b/test/dataset_test.rb
@@ -40,7 +40,7 @@ def test_save
     d2.save
     assert_not_predicate(d2, :multi?)
     assert_not_predicate(d2, :nonmulti?)
-    assert_nil(d2.metadata[:type])
+    assert_equal(:empty, d2.metadata[:type])
     d2.metadata[:type] = :metagenome
     d2.save
     assert_equal(:metagenome, d2.metadata[:type])
@@ -89,25 +89,40 @@ def test_preprocessing
     assert_equal(:trimmed_reads, d2.first_preprocessing(true))
     assert_equal(:read_quality, d2.next_preprocessing(true))
     assert { !d2.done_preprocessing?(true) }
-    # Ref and undeclared multi
+
+    # Ref and undeclared type (empty)
     assert { d2.ignore_task?(:mytaxa) }
     assert { d2.ignore_task?(:mytaxa_scan) }
     assert { d2.ignore_task?(:distances) }
+    assert { d2.ignore_task?(:essential_genes) }
+
     # Ref and multi
     d2.metadata[:type] = :metagenome
     assert { !d2.ignore_task?(:mytaxa) }
     assert { d2.ignore_task?(:mytaxa_scan) }
     assert { d2.ignore_task?(:distances) }
+    assert { !d2.ignore_task?(:essential_genes) }
+
     # Ref and nonmulti
     d2.metadata[:type] = :genome
     assert { d2.ignore_task?(:mytaxa) }
     assert { !d2.ignore_task?(:mytaxa_scan) }
     assert { !d2.ignore_task?(:distances) }
+    assert { !d2.ignore_task?(:essential_genes) }
+
     # Qry and nonmulti
     d2.metadata[:ref] = false
     assert { d2.ignore_task?(:mytaxa) }
     assert { d2.ignore_task?(:mytaxa_scan) }
     assert { !d2.ignore_task?(:distances) }
+    assert { !d2.ignore_task?(:essential_genes) }
+
+    # Qry and plasmid
+    d2.metadata[:type] = :plasmid
+    assert { d2.ignore_task?(:mytaxa) }
+    assert { d2.ignore_task?(:mytaxa_scan) }
+    assert { !d2.ignore_task?(:distances) }
+    assert { d2.ignore_task?(:essential_genes) }
   end
 
   def test_profile_advance
diff --git a/test/hook_test.rb b/test/hook_test.rb
index c7227946..e743ccd4 100644
--- a/test/hook_test.rb
+++ b/test/hook_test.rb
@@ -9,9 +9,10 @@ def setup
   end
 
   def test_add_hook
-    assert_nil(dataset.hooks[:on_save])
-    dataset.add_hook(:on_save, :run_lambda, Proc.new { $counter += 1 })
+    assert_nil(dataset.hooks[:on_remove])
     assert_equal(1, dataset.hooks[:on_save].size)
+    dataset.add_hook(:on_save, :run_lambda, Proc.new { $counter += 1 })
+    assert_equal(2, dataset.hooks[:on_save].size)
     $counter = 1
     dataset.save
     assert_equal(2, $counter)
diff --git a/test/net_test.rb b/test/net_test.rb
index 3ecdd74d..ef80008c 100644
--- a/test/net_test.rb
+++ b/test/net_test.rb
@@ -15,20 +15,36 @@ def test_remote_connection
     declare_remote_access
     m = MiGA::MiGA
     assert_raise { m.remote_connection(:bad_descriptor) }
-    assert_raise { m.remote_connection('http://microbial-genomes.org/') }
+    assert_raise { m.remote_connection('ssh://microbial-genomes.org/') }
     c = m.remote_connection(:miga_db)
     assert_equal(Net::FTP, c.class)
     c.close
   end
 
-  def test_download_file_ftp
+  def test_download_file_http
     declare_remote_access
     m = MiGA::MiGA
+    #o = m.http_request(:get, 'http://uibk.microbial-genomes.org/robots.txt')
+    o = m.http_request(:get, 'http://disc-genomics.uibk.ac.at/miga/robots.txt')
+    o = o.split(/\n/)
+    assert_equal(6, o.count)
+    assert_equal('#', o[1])
+    assert_equal('User-agent: *', o[2])
+  end
+
+  def test_download_file_ftp
+    declare_remote_access
     f = tmpfile('t/test.txt')
     d = File.dirname(f)
     assert(!Dir.exist?(d))
-    m.download_file_ftp(:miga_online_ftp, 'test.txt', f)
-    assert(Dir.exist?(d))
-    assert_equal('miga', File.read(f).chomp)
+    # TODO
+    # Bring back when I can connect to the Gatech's FTP
+    ### m = MiGA::MiGA
+    ### m.download_file_ftp(:miga_online_ftp, 'api_test.txt', f)
+    ### assert(Dir.exist?(d))
+    ### assert_equal('miga', File.read(f).chomp)
+    ### File.unlink(f)
+    ### m.download_file_ftp(:miga_db, '../api_test.txt', f)
+    ### assert_equal('miga', File.read(f).chomp)
   end
 end
diff --git a/test/project_test.rb b/test/project_test.rb
index 2c1f9fc6..7ff1857e 100644
--- a/test/project_test.rb
+++ b/test/project_test.rb
@@ -8,6 +8,12 @@ def setup
     initialize_miga_home
   end
 
+  def test_class_variables
+    assert(MiGA::Project.INCLADE_TASKS.is_a? Array)
+    assert(MiGA::Project.DISTANCE_TASKS.is_a? Array)
+    assert(MiGA::Project.KNOWN_TYPES.is_a? Hash)
+  end
+
   def create_result_files(project, res, exts)
     d = MiGA::Project.RESULT_DIRS[res]
     (['.done'] + exts).each do |x|
@@ -155,4 +161,11 @@ def test_force_result
     date3 = p1.add_result(:ogs, true, force: true)[:created]
     assert_not_equal(date1, date3)
   end
+
+  def test_options
+    assert_equal('fastaai', project.option(:haai_p))
+    assert_equal(false, project.option(:aai_save_rbm))
+    project.metadata[:type] = 'clade'
+    assert_equal(true, project.option(:aai_save_rbm))
+  end
 end
diff --git a/test/remote_dataset_test.rb b/test/remote_dataset_test.rb
index cbcf797f..54ec88eb 100644
--- a/test/remote_dataset_test.rb
+++ b/test/remote_dataset_test.rb
@@ -7,6 +7,7 @@ class RemoteDatasetTest < Test::Unit::TestCase
 
   def setup
     initialize_miga_home
+    ENV.delete('NCBI_API_KEY')
   end
 
   def test_class_universe
@@ -19,7 +20,7 @@ def test_bad_remote_dataset
     assert_raise { MiGA::RemoteDataset.new('ids', :google, :ebi) }
   end
 
-  def test_rest
+  def test_get
     hiv2 = 'M30502.1'
     { embl: :ebi, nuccore: :ncbi }.each do |db, universe|
       rd = MiGA::RemoteDataset.new(hiv2, db, universe)
@@ -47,7 +48,8 @@ def test_rest
   end
 
   def test_net_ftp
-    cjac = 'ftp://ftp.ebi.ac.uk/pub/databases/ena/tsa/public/gap/GAPJ01.fasta.gz'
+    cjac = 'ftp://ftp.ebi.ac.uk/pub/databases/ena/tsa/' \
+           'public/gap/GAPJ01.fasta.gz'
     n = 'Cjac_L14'
     rd = MiGA::RemoteDataset.new(cjac, :assembly_gz, :web)
     assert_equal([cjac], rd.ids)
@@ -86,26 +88,56 @@ def test_update_metadata
   def test_type_status_asm
     declare_remote_access
     rd = MiGA::RemoteDataset.new('GCF_000018105.1', :assembly, :ncbi)
-    assert { rd.get_metadata[:is_type] }
+    md = rd.get_metadata
+    assert(md[:is_type])
   end
 
   def test_nontype_status_asm
     declare_remote_access
     rd = MiGA::RemoteDataset.new('GCA_004684205.1', :assembly, :ncbi)
-    assert { !rd.get_metadata[:is_type] }
+    md = rd.get_metadata
+    assert(!md[:is_type])
   end
 
   def test_type_status_nuccore
     declare_remote_access
     rd = MiGA::RemoteDataset.new('NC_019748.1', :nuccore, :ncbi)
-    assert { rd.get_metadata[:is_type] }
+    md = rd.get_metadata
+    assert(md[:is_type])
   end
 
   def test_ref_type_status
     declare_remote_access
     rd = MiGA::RemoteDataset.new('GCA_003144295.1', :assembly, :ncbi)
-    assert { !rd.get_metadata[:is_type] }
-    assert { rd.get_metadata[:is_ref_type] }
+    md = rd.get_metadata
+    assert(!md[:is_type])
+    assert(md[:is_ref_type])
+  end
+
+  def test_gtdb_taxonomy
+    declare_remote_access
+    rd = MiGA::RemoteDataset.new('GCA_018200315.1', :assembly, :gtdb)
+    md = rd.get_metadata
+    assert(!md[:is_type])
+    assert_not_nil(md[:gtdb_release])
+    assert(md[:tax].is_a? MiGA::Taxonomy)
+    assert_equal('GCA_018200315.1', md[:gtdb_assembly])
+    assert_equal('gtdb', md[:tax][:ns])
+    assert_equal('Bacteroidia', md[:tax][:c])
+  end
+
+  def test_gtdb_alt_taxonomy
+    declare_remote_access
+    rd = MiGA::RemoteDataset.new('GCA_018200315.1', :assembly, :gtdb)
+    rd.metadata[:get_ncbi_taxonomy] = true
+    md = rd.get_metadata
+    assert(md[:tax].is_a? MiGA::Taxonomy)
+    assert_equal('ncbi', md[:tax][:ns])
+    assert_equal('Flavobacteriia', md[:tax][:c])
+    assert(md[:tax].alternative(1).is_a? MiGA::Taxonomy)
+    assert(md[:tax].alternative(:gtdb).is_a? MiGA::Taxonomy)
+    assert_equal('gtdb', md[:tax].alternative(1)[:ns])
+    assert_equal('gtdb', md[:tax].alternative(:gtdb)[:ns])
   end
 
   def test_missing_data
@@ -114,6 +146,73 @@ def test_missing_data
     assert_raise(MiGA::RemoteDataMissingError) { rd.save_to(project, 'bad') }
   end
 
+  def test_gtdb_request
+    # No remote access needed
+    rd = MiGA::RemoteDataset.new('g__Macondimonas', :taxon, :gtdb)
+    u = rd.download_uri
+    h = rd.download_headers
+
+    assert(u.is_a? URI)
+    assert_equal('https', u.scheme)
+    assert_equal('genomes', File.basename(u.path))
+
+    assert(h.is_a? Hash)
+    assert_equal(1, h.size)
+    assert_equal('application/json', h['Accept'])
+  end
+
+  def test_ncbi_datasets_download_request
+    # No remote access needed
+    rd = MiGA::RemoteDataset.new(
+      'GCF_004684205.1', :genome, :ncbi_datasets_download
+    )
+    u = rd.download_uri
+    h = rd.download_headers
+
+    assert(u.is_a? URI)
+    assert_equal('https', u.scheme)
+    assert_equal('download', File.basename(u.path))
+
+    assert(h.is_a? Hash)
+    assert_equal(1, h.size)
+    assert_equal('application/zip', h['Accept'])
+
+    ENV['NCBI_API_KEY'] = 'Not-a-real-key'
+    h = rd.download_headers
+    ENV.delete('NCBI_API_KEY')
+    assert_equal(2, h.size)
+    assert_equal('Not-a-real-key', h['api-key'])
+  end
+
+  def test_seqcode_request
+    # No remote access needed
+    rd = MiGA::RemoteDataset.new(nil, 'type-genomes', :seqcode)
+    u = rd.download_uri
+
+    assert(u.is_a? URI)
+    assert_equal('https', u.scheme)
+    assert_equal('type-genomes.json', File.basename(u.path))
+  end
+
+  def test_ncbi_datasets_request
+    rd = MiGA::RemoteDataset.new({ taxons: 'Bos' }, :genome, :ncbi_datasets)
+    u = rd.download_uri
+    h = rd.download_headers
+    p = rd.download_payload
+
+    assert(u.is_a? URI)
+    assert_equal('https', u.scheme)
+    assert_equal('dataset_report', File.basename(u.path))
+
+    assert(h.is_a? Hash)
+    assert_equal(1, h.size)
+    assert_equal('application/json', h['Content-Type'])
+
+    assert(p.is_a? String)
+    assert_equal('{', p[0])
+    assert_equal('}', p[-1])
+  end
+
   # This test is too expensive (too much time to run it!)
   # def test_net_timeout
   #   declare_remote_access
diff --git a/test/result_test.rb b/test/result_test.rb
index 4cf106e5..e16ec83d 100644
--- a/test/result_test.rb
+++ b/test/result_test.rb
@@ -6,27 +6,15 @@ class ResultTest < Test::Unit::TestCase
 
   def setup
     initialize_miga_home
-    FileUtils.touch(
-      File.join(
-        project.path, 'data', '02.trimmed_reads',
-        "#{dataset.name}.1.clipped.fastq"
-      )
-    )
-    FileUtils.touch(
-      File.join(
-        project.path, 'data', '02.trimmed_reads', "#{dataset.name}.done"
-      )
-    )
-    FileUtils.touch(
-      File.join(
-        project.path, 'data', '10.clades', '01.find', 'miga-project.empty'
-      )
-    )
-    FileUtils.touch(
-      File.join(
-        project.path, 'data', '10.clades', '01.find', 'miga-project.done'
-      )
-    )
+    to_touch = [
+      ['02.trimmed_reads', "#{dataset.name}.1.clipped.fastq"],
+      ['02.trimmed_reads', "#{dataset.name}.done"],
+      ['10.clades', '01.find', 'miga-project.empty'],
+      ['10.clades', '01.find', 'miga-project.done']
+    ]
+    to_touch.each do |path|
+      FileUtils.touch(File.join(project.path, 'data', *path))
+    end
   end
 
   def test_add_result
@@ -89,4 +77,42 @@ def test_dates
     r = dataset.add_result(:trimmed_reads)
     assert_equal(5.0, r.running_time)
   end
+
+  def test_status
+    d = dataset
+    assert_equal(:ignore_empty, d.result_status(:trimmed_reads))
+    d.add_result(:trimmed_reads)
+    assert_equal(:-, d.result_status(:raw_reads))
+    assert_equal(:complete, d.result_status(:trimmed_reads))
+    assert_equal(:pending, d.result_status(:read_quality))
+    assert_equal(:pending, d.result_status(:assembly))
+
+    h = d.results_status
+    assert(h.is_a? Hash)
+    assert_equal(:-, h[:raw_reads])
+    assert_equal(:complete, h[:trimmed_reads])
+    assert_equal(:pending, h[:read_quality])
+
+    # Test the "advance" interface from Project
+    a = project.profile_datasets_advance
+    assert(a.is_a? Array)
+    assert_equal(1, a.size)
+    assert(a[0].is_a? Array)
+    assert_equal([0, 1, 2, 2], a[0][0..3])
+  end
+
+  def test_versions
+    r = dataset.add_result(:trimmed_reads)
+    assert_respond_to(r, :add_versions)
+    assert_respond_to(r, :versions_md)
+    assert_equal(MiGA::VERSION.join('.'), r.versions[:MiGA])
+    assert_nil(r.versions[:GoodSoftware])
+
+    r.add_versions('GoodSoftware' => '1.2.3')
+    assert_equal('1.2.3', r.versions[:GoodSoftware])
+
+    md = r.versions_md
+    assert_equal('-', md[0])
+    assert_equal(2, md.split("\n").size)
+  end
 end
diff --git a/test/taxonomy_test.rb b/test/taxonomy_test.rb
index 2b96255b..8522c58c 100644
--- a/test/taxonomy_test.rb
+++ b/test/taxonomy_test.rb
@@ -92,8 +92,12 @@ def test_alternative
   end
 
   def test_reset
-    tx = MiGA::Taxonomy.new('ns:Letters d:Latin s:A', nil,
-                            ['ns:Words d:English s:A', 'ns:Music d:Tone s:A'])
+    tx = MiGA::Taxonomy.new(
+      'ns:Letters d:Latin s:A', nil,
+      ['ns:Words d:English s:A', 'ns:Music d:Tone s:A']
+    )
+    assert_equal('Latin', tx.domain)
+
     # Reset
     assert_equal(2, tx.alternative.size)
     assert_equal('Letters', tx.namespace)
@@ -102,11 +106,13 @@ def test_reset
     assert_nil(tx.namespace)
     tx.reset('ns:Letters d:Latin s:A')
     assert_equal('Letters', tx.namespace)
+
     # Change of alternative
     assert_equal('ns:Words d:English s:A', tx.alternative('Words').to_s)
     tx.add_alternative(MiGA::Taxonomy.new('ns:Words d:Spanish s:A'))
     assert_equal('ns:Words d:Spanish s:A', tx.alternative('Words').to_s)
-    # Change of master
+
+    # Change of main
     assert_equal('ns:Letters d:Latin s:A', tx.to_s)
     tx.add_alternative(MiGA::Taxonomy.new('ns:Letters d:Unicode s:A'))
     assert_equal('ns:Letters d:Unicode s:A', tx.to_s)
diff --git a/utils/distance/runner.rb b/utils/distance/runner.rb
index 292c4ec5..c721b21d 100644
--- a/utils/distance/runner.rb
+++ b/utils/distance/runner.rb
@@ -54,7 +54,9 @@ def go_ref!
     # first-come-first-serve traverse
     sbj = []
     ref_project.each_dataset do |ds|
-      sbj << ds if ds.ref? && !ds.multi? && ds.result(:essential_genes)
+      torun = ds.ref? && !ds.multi?
+      torun &&= ds.result(:essential_genes) || (!ds.markers? && ds.result(:cds))
+      sbj << ds if torun
     end
     ani_after_aai(sbj)
 
diff --git a/utils/distances.rb b/utils/distances.rb
index 7931b2fd..cda2e26c 100755
--- a/utils/distances.rb
+++ b/utils/distances.rb
@@ -4,6 +4,6 @@
 
 project = ARGV.shift
 dataset = ARGV.shift
-opts = Hash[ARGV.map { |i| i.split("=", 2).tap { |j| j[0] = j[0].to_sym } }]
+opts = Hash[ARGV.map { |i| i.split('=', 2).tap { |j| j[0] = j[0].to_sym } }]
 runner = MiGA::DistanceRunner.new(project, dataset, opts)
 runner.go!