https://github.com/brentp/goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
https://github.com/brentp/goleft

bioinformatics coverage depth genomics golang

Last synced: 26 days ago
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goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

• Host: GitHub
• URL: https://github.com/brentp/goleft
• Owner: brentp
• License: mit
• Created: 2016-09-19T15:28:40.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-04-19T13:40:03.000Z (about 2 months ago)
• Last Synced: 2024-05-01T22:46:25.691Z (about 2 months ago)
• Topics: bioinformatics, coverage, depth, genomics, golang
• Language: Go
• Homepage:
• Size: 5.09 MB
• Stars: 207
• Watchers: 16
• Forks: 24
• Open Issues: 14
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md
  • License: LICENSE

Lists

• awesome-bio-go - goleft

README

        

# goleft

[![Build Status](https://travis-ci.org/brentp/goleft.svg)](https://travis-ci.org/brentp/goleft)

goleft is a collection of bioinformatics tools written in

[go](https://github.com/golang/go) distributed together

as a single binary under a liberal (MIT) license.

Running the binary `goleft` will give a list of subcommands

with a short description. Running any subcommand without

arguments will give a full help for that command.

# Installation

The easiest way to install goleft is to download the latest binary from

the [releases](https://github.com/brentp/goleft/releases) and make sure to chmod +x the resulting binary.

If you are using [go](https://github.com/golang/go), you can build from source with:

```

go get -u github.com/brentp/goleft/...

go install github.com/brentp/goleft/cmd/goleft

```

`goleft` is also available in [bioconda](https://bioconda.github.io)

# Commands

+ [covstats](https://github.com/brentp/goleft/tree/master/covstats#covstats)   : estimate coverage and insert-size statistics on bams by sampling

+ [depth](https://github.com/brentp/goleft/tree/master/depth#depth)    : parallelize calls to samtools in user-defined windows

+ depthwed : matricize output from depth to n-sites * n-samples

+ [indexcov](https://github.com/brentp/goleft/tree/master/indexcov#indexcov) : quick coverage estimate using only the bam index

+ [indexsplit](https://github.com/brentp/goleft/tree/master/indexsplit#indexsplit) : generate regions of even data across a cohort (for parallelization)

+ [samplename](https://github.com/brentp/goleft/tree/master/samplename#samplename): report samplename(s) from a bam's SM tag