bioawk

AWK with bioinformatics extensions

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.

Versions: 1.0
Website: https://github.com/lh3/bioawk
Licenses: X11
Package source: gnu/packages/bioinformatics.scm
Builds: See build status
Issues: See known issues

Installation

Install the latest version of bioawk as follows:

guix install bioawk

Or install a particular version:

guix install bioawk@1.0

You can also install packages in augmented, pure or containerized environments for development or simply to try them out without polluting your user profile. See the guix shell documentation for more information.