isabella232 / bionode-bwa

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

bionode.io

bionode-bwa

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

[![Build Status][travis-image]][travis-url]

Install

You need to install the latest Node.JS first, please check nodejs.org or do the following:

# Ubuntu
sudo apt-get install npm
# Mac
brew install node
# Both
npm install -g n
n stable

To use bionode-bwa as a command line tool, you can install it globally with -g.

npm install bionode-bwa -g

Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the node_modules directory by doing the same command without -g.

npm i bionode-bwa # 'i' can be used as shorcut to 'install'

Usage

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

var bwa = require('bionode-bwa')
// aligment path is optional, reads name used instead with sam suffix
bwa('reference.fasta.gz', 'reads.fastq.gz', 'alignment.sam')
.on('data', console.log)

var options = {
  operation: 'mem',
  params: '-t 4'
}
var stream = bwa(options) // Use BWA mem algorithm with 4 threads
var obj = {
  reference: 'reference.fasta.gz',
  reads: ['reads.fastq.gz']
}
stream.write(obj)

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 reference.fasta.gz reads.fastq.gz --alignment out.sam
$ echo '{"reference": "ref.fasta.gz", "reads": "[p1.fq, p2.fq]"}' | bionode-bwa  -

Contributing

We welcome all kinds of contributions at all levels of experience, please read the CONTRIBUTING.md to get started!

Communication channels

Don't be shy! Come talk to us 😃

• Email [email protected]
• Chat room http://gitter.im/bionode/bionode
• IRC #bionode on Freenode
• Twitter @bionode