brentp/goleft brentp/goleft

  • Stars
    star
    202
  • Rank 193,691 (Top 4 %)
  • Language
    Go
  • License
    MIT License
  • Created over 8 years ago
  • Updated about 2 years ago
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brentp/goleft
github

brentp

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Repository Details

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

goleft

Build Status

goleft is a collection of bioinformatics tools written in 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 and make sure to chmod +x the resulting binary.

If you are using 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

Commands

  • covstats : estimate coverage and insert-size statistics on bams by sampling
  • depth : parallelize calls to samtools in user-defined windows
  • depthwed : matricize output from depth to n-sites * n-samples
  • indexcov : quick coverage estimate using only the bam index
  • indexsplit : generate regions of even data across a cohort (for parallelization)
  • samplename: report samplename(s) from a bam's SM tag

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