bionode.io

bionode-bwa

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


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Install
-------

Install bionode-bwa with npm:

``sh
$ 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:

`js
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)
`

`js
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.

$3


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

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:

`sh
$ npm test
`

Please also check for code coverage:

`sh
$ npm run coverage
`

To rebuild the documentation using the comments in the code:

`sh
$ npm run build-docs
``
Check the issues for ways to contribute.

Contacts
--------
Bruno Vieira <mail@bmpvieira.com> @bmpvieira
For BWA support contact Heng Li

License
-------

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

[npm-url]: http://npmjs.org/package/bionode-bwa
[npm-image]: http://img.shields.io/npm/v/bionode-bwa.svg?style=flat-square
[travis-url]: http:////travis-ci.org/bionode/bionode-bwa
[travis-image]: http://img.shields.io/travis/bionode/bionode-bwa.svg?style=flat-square
[coveralls-url]: http:////coveralls.io/r/bionode/bionode-bwa
[coveralls-image]: http://img.shields.io/coveralls/bionode/bionode-bwa.svg?style=flat-square
[depstat-url]: http://david-dm.org/bionode/bionode-bwa
[depstat-image]: http://img.shields.io/david/bionode/bionode-bwa.svg?style=flat-square
[js-standard-style-url]: https://github.com/feross/standard
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[waffle-image]: https://badge.waffle.io/bionode/bionode-bwa.png?label=ready&title=issues%20ready
[waffle-url]: https://waffle.io/bionode/bionode-bwa
[doi-url]: http://dx.doi.org/10.5281/zenodo.11487
[doi-image]: http://img.shields.io/badge/doi-10.5281/zenodo.11487-blue.svg?style=flat-square