seqtk1
Sampling, trimming, fastq2fasta, subsequence, reverse complement
Usage
seqtk <command>
<arguments>
Overview
Currently, seqtk supports quality based trimming with the phred algorithm, converting fastq to fasta, reverse complementing sequences, extracting or masking subsequences in regions given in a BED/name list file, and more. It contains a subsampling module to sample exactly n sequences or a fraction of sequences.
Seqtk supports both fasta and fastq input files, which can be optionally gzip compressed.
Commands
Command: seq common transformation of FASTA/Q
comp
|
get the nucleotide composition of FASTA/Q |
|---|---|
sample
|
subsample sequences |
subseq
|
extract subsequences from FASTA/Q |
trimfq
|
trim FASTQ using the Phred algorithm |
hety
|
regional heterozygosity |
mutfa
|
point mutate FASTA at specified positions |
mergefa
|
merge two FASTA/Q files |
randbase
|
choose a random base from hets |
cutN
|
cut sequence at long N |
listhet
|
extract the position of each het |
Releases
Unchanged in 6 releases since Debian 8 (Jessie).