Table of Contents



Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.


  • Seqtk version 1.3-r106 is available in Puhti


Seqtk in included in the biokit module:

module load biokit

Seqtk command syntax is:

seqtk <command> <arguments>

The available seqtk commands are:

Command Function
seq common transformation of FASTA/Q
comp get the nucleotide composition of FASTA/Q
sample subsample sequences
subseq extract subsequences from FASTA/Q
fqchk fastq QC (base/quality summary)
mergepe interleave two PE FASTA/Q files
trimfq trim FASTQ using the Phred algorithm
hety regional heterozygosity
gc identify high- or low-GC regions
mutfa point mutate FASTA at specified positions
mergefa merge two FASTA/Q files
famask apply a X-coded FASTA to a source FASTA
dropse drop unpaired from interleaved PE FASTA/Q
rename rename sequence names
randbase choose a random base from hets
cutN cut sequence at long N
listhet extract the position of each het


Convert FASTQ to FASTA:

seqtk seq -a in.fq.gz > out.fa

Extract sequences with names in file name.lst, one sequence name per line:

seqtk subseq in.fq name.lst > out.fq

Extract sequences in regions contained in file reg.bed:

seqtk subseq in.fa reg.bed > out.fa