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Minor edits to BLAST notebook
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willbradshaw committed Jan 30, 2024
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<p><a href="./notebooks/2024-01-30_blast-validation.html"> <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div> </a></p>
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4 changes: 2 additions & 2 deletions docs/notebooks/2024-01-30_blast-validation.html
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<p>In summary, using command-line <code>blastn -remote,</code> combined with tabular processing in R against a reference class of all viral taxids, works well as a substitute for manual inspection of online BLAST results for validating human-viral read assignments. It’s too slow and failure-prone to be added to the pipeline as a replacement or supplement to the Bowtie/Kraken automated approach, but will be my go-to approach in future for manual validation and refinement of human-viral assignment criteria.</p>
<p>In summary, using command-line <code>blastn -remote,</code> combined with tabular processing in R against a reference class of all viral taxids, works well as a substitute for manual inspection of online BLAST results for validating human-viral read assignments. It’s too slow and failure-prone to be added to the pipeline as a replacement or supplement to the Bowtie/Kraken automated approach, but will be my go-to approach in future for manual validation and refinement of human-viral assignment criteria – at least until I’m able to try out Elastic-BLAST.</p>


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<span id="cb5-235"><a href="#cb5-235" aria-hidden="true" tabindex="-1"></a>blast_performance_qcov</span>
<span id="cb5-236"><a href="#cb5-236" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
<span id="cb5-237"><a href="#cb5-237" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-238"><a href="#cb5-238" aria-hidden="true" tabindex="-1"></a>In summary, using command-line <span class="in">`blastn -remote,`</span> combined with tabular processing in R against a reference class of all viral taxids, works well as a substitute for manual inspection of online BLAST results for validating human-viral read assignments. It's too slow and failure-prone to be added to the pipeline as a replacement or supplement to the Bowtie/Kraken automated approach, but will be my go-to approach in future for manual validation and refinement of human-viral assignment criteria.</span>
<span id="cb5-238"><a href="#cb5-238" aria-hidden="true" tabindex="-1"></a>In summary, using command-line <span class="in">`blastn -remote,`</span> combined with tabular processing in R against a reference class of all viral taxids, works well as a substitute for manual inspection of online BLAST results for validating human-viral read assignments. It's too slow and failure-prone to be added to the pipeline as a replacement or supplement to the Bowtie/Kraken automated approach, but will be my go-to approach in future for manual validation and refinement of human-viral assignment criteria – at least until I'm able to try out Elastic-BLAST.</span>
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