• Seqfilter Seqfilter is a small tool written in C on top of the excellent [[https://github.com/attractivechaos/klib][klib]] library by Heng Li. It allows filtering of fasta and fastq files based on sequence IDs and sequence length. The fasta and fastq input files may be gzipped.

• Get it!

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  git clone --recursive https://github.com/clwgg/seqfilter

cd seqfilter make

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• Usage Seqfilter will always try to filter by IDs, since thats its intended purpose. You can however omit the ID file. In that case, you have to specify the '-n' flag for negative filtering if you want to produce output, to allow output of sequences without a "valid" ID.

Negative filtering ('-n') means that all sequences without ID matches are kept (subsequently, if no ID file is supplied, all sequences are without ID matches).

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filter by ID file

seqfilter -i in.fq -l ids.txt -o out.fq

filter by ID file and min length 30

seqfilter -m 30 -i in.fq -l ids.txt -o out.fq

filter only by min length 30

seqfilter -n -m 30 -i in.fq -o out.fq

keep only sequence called "mt"

seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa

remove sequence called "mt" from input

seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

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