Seqtk

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
- License
- Available
- Usage
  - Examples
- More information

License

Free to use and open source under MIT License.

Available

Puhti: 1.3-r106, 1.4

Usage

Seqtk is included in the biokit module:

module load biokit

Alternatively, Seqtk can be loaded as an independent module:

module load seqtk/<version>

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`	sub-sample 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 an 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

Examples

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

More information

Seqtk home page

Last update: July 17, 2024