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.
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