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torognes / vsearch

Versatile open-source tool for microbiome analysis
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missing userfields options #548

Open frederic-mahe opened 7 months ago

frederic-mahe commented 7 months ago

As a follow-up on issue #545, here is a list of --userfields options available in usearch (see userfields), but not in vsearch.

Starting with the most important, in my opinion:

diffs       Number of differences (gaps + mismatches).
mid         Fraction of letter pairs that match.
qseq        Full-length query sequence.
tseq        Full-length target sequence.
qrowdots    Aligned query segment with gaps and dots for matched positions.
trowdots    Aligned target segment with gaps and dots for matched positions.

These other options are less important, or are specific to commands not yet available in vsearch:

abskew      Abundance skew.
clusternr   Cluster number.
qlor        0-based query start coordinate.
qhir        0-based query end coordinate.
tlor        0-based target start coordinate.
thir        0-based target end coordinate.
orflo       Start coordinate of query ORF in nt sequence.
orfhi       End coordinate of query ORF in nt sequence.
orfframe    Frame of query ORF.