defaultsettings.Rmd

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# iMAP Default Settings {#defaultsettings}

>iMAP users who want to change the default settings may do so using any text editor. The table below shows the location of default parameters that may be altered</h3>


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<th align="left"><strong>Parameter to change</strong></th>
<th align="left"><strong>File Path</strong></th>
<th align="left"><strong>Filename</strong></th>
<th align="left"><strong>Default setting</strong></th>
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<td align="left">Phred score</td>
<td align="left">iMAP/code/preprocessing</td>
<td align="left">04_get_highscore_reads.bash</td>
<td>trimq=25</td>
</tr>
<tr>
<td align="left">Min Contig length</td>
<td align="left">iMAP/code/seqprocessing</td>
<td align="left">01_assemble_paired_reads.batch</td>
<td>minlength=100</td>
</tr>
<tr>
<td align="left">Max Contig length</td>
<td align="left">iMAP/code/seqprocessing</td>
<td align="left">01_assemble_paired_reads.batch</td>
<td>maxlength=300</td>
</tr>
<tr>
<td align="left">Min alignment length</td>
<td align="left">iMAP/code/seqprocessing</td>
<td align="left">02_align_for_16S_consensus.batch</td>
<td>minlength=100</td>
</tr>
<tr>
<td align="left">Max alignment length</td>
<td align="left">iMAP/code/seqprocessing</td>
<td align="left">02_align_for_16S_consensus.batch</td>
<td>maxlength=300</td>
</tr>
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<td align="left">Reference</td>
<td align="left">iMAP/code/seqclassification</td>
<td align="left">01_classify_seqs.batch</td>
<td>silva.seed.ng.fasta; QIIME2</td>
</tr>
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<td align="left">Taxonomy</td>
<td align="left">iMAP/code/seqclassification</td>
<td align="left">01_classify_seqs.batch</td>
<td>silva.seed.tax</td>
</tr>
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<td align="left">Classification cutoff</td>
<td align="left">iMAP/code/seqclassification</td>
<td align="left">01_classify_seqs.batch</td>
<td>cutoff=80</td>
<tr>
<td align="left">QIIME2 DADA2 settings</td>
<td align="left">iMAP/code/qiime2</td>
<td align="left">qiime2.bash</td>
<td>DADA2 QC parameters are set at 0</td>
</tr>
<tr>
<td align="left">QIIME2 Taxonomy classifier</td>
<td align="left">iMAP/code/qiime2</td>
<td align="left">qiime2.bash</td>
<td>gg-13-8-99-515-806-nb-classifier.qza</td>
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