bioawk
Link to section 'Introduction' of 'bioawk' Introduction
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzipped BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
For more information, please check its website: https://biocontainers.pro/tools/bioawk and its home page on Github.
Link to section 'Versions' of 'bioawk' Versions
- 1.0
Link to section 'Commands' of 'bioawk' Commands
- bioawk
Link to section 'Module' of 'bioawk' Module
You can load the modules by:
module load biocontainers
module load bioawk
Link to section 'Example job' of 'bioawk' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Bioawk on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bioawk
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bioawk
bioawk -c fastx '{print ">"$name;print revcomp($seq)}' seq.fa.gz