fastats

README

Fastats

Tools for bioinformatics in Go

Intro

This package contains a large number of utility scripts for more easily writing bioinformatics programs in Go. Most notably, it contains parsers and printers for most of the major bioinformatics file types, including fasta, fastq, gff, gtf, bed, newick, and sam. It also contains a set of executables made with these tools to do common bioinformatics tasks. For example, the "fastats" executable prints contiguity statistics (N50, etc.) for fasta files.

Dependencies

This package depends on several other Go packages maintained by me. See the file "go.mod" for more info.

Library installation

To install the latest version of this library, just use:

go get github.com/jgbaldwinbrown/fastats/pkg

Then, to install any of the command line tools, do the following:

cd fastats
go install cmd/[tool]

If that doesn't work, manually install the tool as follows:

cd fastats
go build cmd/[tool]/[tool].go
cp [tool] /usr/bin/