Comments (2)
gwarmstrong
commented on July 26, 2024
2
@nbokulich thanks for the input! query coverage, and classify-consensus-vsearch were awesome for helping me get some things figured out.
I think I can meet my criteria just by exposing --leftjust from vsearch, and setting --id 1.0.
Thanks!
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nbokulich
commented on July 26, 2024
1
maybe just expose the query coverage and subject coverage parameters? it seems like adding options to exclude-seqs would get this done.
Maybe also check out the classify-consensus-vsearch method in q2-feature-classifier in case it is less work to modify that method (i.e., you would essentially do a taxonomic classification and anything that does not classify, i.e., align gets filtered out)
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Related Issues (20)
- _blast.py suggestions HOT 1
- test additions
- `evaluate_seqs`: add `max-accepts` parameter
- `evaluate_seqs`: add optional input of `FeatureData[Taxonomy]` for labeling features
- `evaluate_composition`: multiple score plots in viz?
- `evaluate_composition`: fix _validate_metadata_values_are_subset error message
- Add Citations
- convert `evaluate_*` visualizers to pipelines
- `evaluate_composition`: add bray-curtis dissimilarity
- BUG: TAR/TDR values are getting switched
- `evaluate-seqs`: replace histograms with scatterplot of similarity X coverage X abundance
- exclude-seqs vsearch fails to parse with imported fasta HOT 1
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- IMP: expose 'strand' argument to `exclude-seqs`
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- ENH: add MCC to evaluation metrics
- `filter_reads` returns no sequences on single-end reads input HOT 1
- Hyphens in metadata columns not consistently converted to R dot syntax in decontam-identify
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