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        <tspan x="2264.7" y="1436.51">DIAMOND blastx</tspan>
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    <tspan x="2735.06" y="1543.82">Reads R1 and R2 are merged together but they don't overlap</tspan>
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      <tspan x="2478.12" y="1100.51">1) Trying to find overlap between R1 &amp; R2 and merge them;</tspan>
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      <tspan x="3173.7" y="1107.59">2) Searching for &lt;model_adapter_sequence_5prime&gt;</tspan>
      <tspan x="3173.7" y="1123.59">[tcNNNGGAGCTGTCGTATTCCAGTCAGG]</tspan>
      <tspan x="3173.7" y="1139.59">to identify 3 bases of barcodes accepting a </tspan>
      <tspan x="3173.7" y="1155.59">maximum mismatch (-mm 1);</tspan>
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      <tspan x="3173.7" y="1190.27">3) Searching for &lt;model_adapter_sequence_3prime&gt; </tspan>
      <tspan x="3173.7" y="1206.27">[CCTCTAAACGGGTCTTGAGGGGTT] to trim off the read tail;</tspan>
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        <tspan x="2490.4" y="1138.7">PEAR, vsearch or usearch can be used to find overlapping bases between reads from the same fragment (R1 &amp; R2). </tspan>
        <tspan x="2490.4" y="1154.7">doi:10.1093/bioinformatics/btt593</tspan>
        <tspan x="2490.4" y="1170.7"></tspan>
        <tspan x="2490.4" y="1186.7">The following are used in the execution but are not configurable parameters:</tspan>
        <tspan x="2490.4" y="1202.7">PEAR: --keep-original ; vsearch: --fastq_mergepairs ; usearch: --fastq_mergepairs</tspan>
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        <tspan x="2484.82" y="1242.59">There are 3 options to deal with reads R1 and R2 (of the same fragment) with no overlap</tspan>
        <tspan x="2484.82" y="1258.59"> </tspan>
        <tspan x="2484.82" y="1274.59">- Use the protein database to scaffold the R1 and R2 reads, so the reads are concatenated together and splitted by a gap, which the length corresponds to the exact number of </tspan>
        <tspan x="2484.82" y="1290.59">   bases considering the reads' mapping against a protein. This is possible when a match exists, when the match is not coherent, only the R1 read is retained. The read alignments</tspan>
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        <tspan x="2484.82" y="1418.59">- Retain only the R1 read;</tspan>
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        <tspan x="2484.82" y="1450.59">- The reads R1 and R2 are concatenated together and splitted by a number of N's (five for example, NNNNN).  In this case, the R2 was reverse complemented to stay in Forward </tspan>
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          <tspan x="3325.72" y="1365.77">TEMPORARY </tspan>
          <tspan x="3325.72" y="1381.77">DIAMOND blastx </tspan>
          <tspan x="3325.72" y="1397.77">OUTPUT files</tspan>
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          <tspan x="2806.53" y="1365.66">[PEAR/usearch/vsearch] output</tspan>
          <tspan x="2806.53" y="1381.66">*.unassembled.forward.fastq</tspan>
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      <tspan x="4355.3" y="3060.18">Filtering proteins based on these parameters:</tspan>
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      <tspan x="4355.3" y="3108.18">-u : Minimum number of target groups with any evidence accounted (-m); </tspan>
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      <tspan x="917.801" y="1641.61">demux_PEP-Seq.pl OUTPUT FILES:</tspan>
      <tspan x="917.801" y="1657.61"></tspan>
      <tspan x="917.801" y="1673.61">WRONGTEMPLATE - Not found a valid alignment (score&gt;=30) with  </tspan>
      <tspan x="917.801" y="1689.61">the template sequence: tcNNNGGAGCTGTCGTATTCCAGTCAGG;</tspan>
      <tspan x="917.801" y="1705.61"></tspan>
      <tspan x="917.801" y="1721.61">UNIDENTIFIED - Not found a valid 3 bases of DNA barcode, i.e., the </tspan>
      <tspan x="917.801" y="1737.61">mismatches exceed the stablished maximum (-mm 1);</tspan>
      <tspan x="917.801" y="1753.61"></tspan>
      <tspan x="917.801" y="1769.61">AMBIGUOUS - A valid 3 bases match was found with more than </tspan>
      <tspan x="917.801" y="1785.61">one expected DNA barcode from the barcode list;</tspan>
      <tspan x="917.801" y="1801.61"></tspan>
      <tspan x="917.801" y="1817.61">REFUSED - the read length is smaller than 60 bp;</tspan>
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