bionode-bwa

bionode.io

# bionode-bwa [![NPM version][npm-image]][npm-url] [![Build Status][travis-image]][travis-url] [![Coveralls Status][coveralls-image]][coveralls-url] [![Dependency Status][depstat-image]][depstat-url] [![DOI][doi-image]][doi-url]

A Node.js wrapper for the Burrow-Wheeler Aligner (BWA).

Install

Install bionode-bwa with npm:

$ npm install bionode-bwa

To use it as a command line tool, you can install it globally by adding -g .

Usage

If you're using bionode-bwa with Node.js, you can require the module:

var bwa = require('bionode-bwa')
var mem = bwa('mem -t 4') // Use BWA mem algorithm with 4 threads
mem('reference.fasta.gz reads.fastq.gz alignment.sam')
.on('data', console.log)

Please read the documentation for the methods exposed by bionode-bwa.
Check BWA's documentation for the arguments that can be passed.

Command line examples

$ bionode-bwa mem reference.fasta.gz reads.fastq.gz alignment.sam
$ bionode-bwa mem -t 4 reference.fasta.gz reads.fastq.gz

Contributing

To contribute, clone this repo locally and commit your code on a separate branch.

Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:

$ npm test

Please also check for code coverage:

$ npm run coverage

To rebuild the documentation using the comments in the code:

$ npm run build-docs

Check the issues for ways to contribute.

Contacts

Bruno Vieira <[e-mail]> @bmpvieira
For BWA support contact Heng Li

License

bionode-bwa is licensed under the MIT license.
Check ChooseALicense.com for details.