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
- Roihu-CPU: 1.4, via the
bio-appsmodule.
Usage
Seqtk is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Seqtk module:
seqtk command syntax is:
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:
Extract sequences with names in file name.lst, one sequence name per line:
Extract sequences in regions contained in file reg.bed:
Run seqtk in an interactive session or as a batch job, not on the login node. See creating a batch job script for Roihu for more information about running batch jobs.