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Improvement Description
Clarify why vsearch does not output the same bitscores and evalues as blast.
Current Behavior
After running a vsearch plugin, all outputs bitscores are all 0 and all evalues -1
📑
Warning, vsearch uses global pairwise alignments, not blast’s seed-and-extend algorithm. Therefore, some common blast output values (alignment start and end, evalue, bit score) are reported differently.
...
evalue: expectancy-value (not computed for nucleotide alignments). Always set to -1.
bits: bit score (not computed for nucleotide alignments). Always set to 0.
Questions
Should we:
Drop these columns from the vsearch output, as they are not useful.
or
Clarify why they are always 0 and -1
We should not drop these columns, as this would break the format (vsearch conveniently outputs a blast6 format output).
Clarification is a better solution, but this is probably better placed in a tutorial (or other documentation) than in q2-feature-classifier. We do not currently have a tutorial for using vsearch-global or classify-consensus-vsearch, but that's where I would put any explanation of the outputs.
Though honestly this is the first time this question was ever asked in the past 6 years, and now there is a great answer by you @colinbrislawn that we can point to on the forum if anyone else asks, so I am not sure that this is an issue that needs to be fixed.
Improvement Description
Clarify why vsearch does not output the same bitscores and evalues as blast.
Current Behavior
After running a vsearch plugin, all outputs bitscores are all 0 and all evalues -1
📑
Questions
Should we:
Drop these columns from the vsearch output, as they are not useful.
or
Clarify why they are always 0 and -1
Comments
forums x-ref
References
vsearch manual pdf search for 'evalue'
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