Problems with seqtk rename on fastq files with long reads (like isoseq)

lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats

MIT License

1.35k stars 310 forks source link

Problems with seqtk rename on fastq files with long reads (like isoseq) #171

Open maol-corteva opened 3 years ago

maol-corteva commented 3 years ago

recently I found that seqtk rename on long reads (not sure which length threshold) produces duplicate IDs for the first 10 sets of sequences (naming them as 1..1..2..2..3..3..4..4..5..5..6..7..8).... However it works fine for short reads.

I have tried in 4 different isoseq runs (standard PacBio isoseq pipe) and all generated same duplicate ids. Using the optional prefix does not affect numbering (problem persists).

Can someone verify this?

maol-corteva commented 3 years ago

BTW, trying older versions of seqtk does not change the result, so if this is an issue, it has been in there for a long time. Still, I don't know if others can replicate what I am seeing.

Cheers... and thanks for the awesome seqtk library.