docs: def find_cross_contamination(databases, pair, tmpdir='tmp', log='log.txt', threads=1):
      """
      Usese mash to find out whether or not a sample has more than one genus present, indicating cross-contamination.
      :param databases: A databases folder, which must contain refseq.msh, a mash sketch that has one representative
      per genus from refseq.
      :param tmpdir: Temporary directory to store mash result files in.
      :param pair: Array with path to forward reads at index 0 and path to reverse reads at index o
      :param log: Logfile to write to.
      :param threads: Number of threads to run mash wit.
      :return: cross_contam: a bool that is True if more than one genus is found, and False otherwise.
      :return: genera_present: A string. If only one genus is found, string is just genus. If more than one genus is found,
      the string is a list of genera present, separated by colons (i.e. for Escherichia and Salmonella found, string would
      be 'Escherichia:Salmonella'. If no genus found, return 'NA'
      """
      genera_present = list()
      out, err, cmd = mash.screen('{}/refseq.msh'.format(databases), pair[0],
                                  pair[1], threads=threads, w='', i='0.95',
                                  output_file=os.path.join(tmpdir, 'screen.tab'), returncmd=True)
      write_to_logfile(log, out, err, cmd)
      screen_output = mash.read_mash_screen(os.path.join(tmpdir, 'screen.tab'))
      for item in screen_output:
          mash_genus = item.query_id.split('/')[-3]
          if mash_genus == 'Shigella':
              mash_genus = 'Escherichia'
          if mash_genus not in genera_present:
              genera_present.append(mash_genus)
      if len(genera_present) == 1:
          genera_present = genera_present[0]
      elif len(genera_present) == 0:
          genera_present = 'NA'
      else:
          tmpstr = ''
          for mash_genus in genera_present:
              tmpstr += mash_genus + ':'
          genera_present = tmpstr[:-1]
      return genera_present