anchor.diff:        <div class="card-supporting-text">
           <p>
             When setup is complete, the analyse script will automatically use the downloaded databases and linked tools.
  -          Here we will run 2 preconfigured pipelines on the same input data.
             The input data consists of a 100 paired-end reads sampled from a dataset
               generated by Lindgreen <i>et al.</i> (2016) for their metabenchmark.
             With these paired-end reads in the <code>sample-1.fq</code> and <code>sample-2.fq</code> files,
  -            the command is as follows.
  +            the commands are as follows.
           </p>
           <pre style="max-height: initial;">
  -<!--   --><b>$</b> umgap-analyse.sh -1 sample-1.fq -2 sample-2.fq -t tryptic-precision -o tryptic-precision-output.fa -1 sample-1.fq -2 sample-2.fq -t tryptic-sensitivity -z -o tryptic-sensitivity-output.fa.gz
  +<!--   --><b>$</b> head -4 sample-1.fq
  +<!--   -->@1198114###CP002480-_Acidobacteria_733918/1
  +<!--   -->ATCGCGCACGCGGCCGATGCCCCAGAAGAGATTGACAGCGGTGGGGCGGGCGGCGGCGAGGTGGTCGCAGATCTCGGCGACCTCTGCGTTGAGGGTCGGG
  +<!--   -->+
  +<!--   -->AADEGGAGIIEIHFHKHJKKJKHIJJIIKCJAHBFKKFHIJIF;JIH5DE$I>CBE$E:FGEJCGABEEECCDKD?D?C$ECEEE;CEEDEEAD=?ED$D
  +<!--   --><b>$</b> umgap-analyse.sh -1 sample-1.fq -2 sample-2.fq -t tryptic-precision -o tryptic-precision-output.fa
   <!--   --><b>$</b> head -2 tryptic-precision-output.fa
  -<!--   --><b>$</b> zcat tryptic-precision-output.fa.gz | head -2</pre>
  +<!--   -->>1198114###CP002480-_Acidobacteria_733918/1_1_100_-
  +<!--   -->1</pre>
  +        <p>
  +          It seems the pipeline cannot be more specific than <emph>root</emph> (Taxon ID 1) for the first read.
  +        </p>
  +        <p>
  +          If you used a non-default configuration directory for setup,
  +           you'll need to pass the same directory here, with the <code>-c</code> option.
  +          When running the pipeline on large samples, it may be useful to compress the output.
  +          Use the <code>-z</code> flag to <span class="initialism">GZIP</span> the results.
  +          Should the input be <span class="initialism">GZIP</span>-compressed,
  +           the script will detect this.
  +          Note that all arguments can be repeated to bundle multiple analysis,
  +           each series ending with a <code>-o</code> option.
  +        </p>
           <dl class='dl-horizontal'>
             <dt><samp>-c dir</samp></dt><dd>Set a different configuration directory.</dd>
             <dt><samp>-z</samp></dt><dd>Request compression of the output file.</dd>
  -          <dt><samp>-1 file</samp></dt><dd>Single ended (or first pair-ended) FASTA or FASTQ input file, optionally compressed.</dd>
  -          <dt><samp>-2 file</samp></dt><dd>Second pair-ended FASTA or FASTQ input file, optionally compressed.</dd>
  +          <dt><samp>-1 file</samp></dt><dd>Single ended FASTA or first pair-ended FASTQ input file, optionally compressed.</dd>
  +          <dt><samp>-2 file</samp></dt><dd>Second pair-ended FASTQ input file, optionally compressed.</dd>
             <dt><samp>-t</samp></dt><dd>Type of the analysis (high precision by default).</dd>
             <dt><samp>-o file</samp></dt><dd>The output file.</dd>
           </dl>
  
positive.code:            but you can also use it to verify the file locations and download newer versions of the data.
            If you're planning to use the tryptic precision, tryptic sensitivity, high precision or max precision pipelines,
             you'll need to <a href="https://github.com/unipept/FragGeneScanPlusPlus/">install FragGeneScan++</a> first.
            In this casestudy, we will use the two tryptic pipelines, so we don't have to download the 9-mer index (~12GiB, rather than ~150GiB).
          </p>
          <p>
            Following code snippet shows the interaction with the setup script.
  
negative.code:       <div class="card-supporting-text">
          <p>
            After analysis, you probably want to view the results.
            While the analyse script output format is easily parsed,
             you can also use the visualize script to create importable CSV frequency tables
             and interactive visualisations.
            The interactive visualisations can be stored locally or hosted online.
            The following snippet creates all three in turn.
          </p>
          <pre style="max-height: initial;">
  <!--   --><b>$</b> umgap-visualize.sh -i tryptic-precision-output.fa -t -r phylum
  <!--   -->2	1117	Cyanobacteria
  <!--   -->4	57723	Acidobacteria
  <!--   -->4	201174	Actinobacteria
  