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bionode

A Node.js JavaScript library for client and server side bioinformatics

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bionode.io

# bionode > Modular and universal bioinformatics

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Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.

Install

Install Node.js (we recommend using n).

If you want to install bionode in your current folder and use the JavaScript API, do:

npm install bionode

If you want to install it globally and use it as a command line tool add -g, like:

npm install bionode -g

The previous commands will install all bionode modules currently available. If you don't need all modules and prefer to be more selective, have a look at the list of modules.

Usage

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

var bionode = require('bionode')

If you're using it as a command line tool, type bionode <module> <command> <arguments>, e.g.:

bionode ncbi search genome solenopsis invicta

Please read the documentation for the methods exposed by bionode.

List of modules

The following are modules available/planned for Bionode.

Name Type Description Status1 People2
ncbi Data access Access to NCBI API (e-utils) production bmpvieira maxogden mafintosh olgabot mlovci
fasta Parser Fasta parser request bmpvieira
seq Wrangling Sequence transformation (reverse complement, etc) request bmpvieira IsmailM yeban
template Documentation Example template module request bmpvieira
JS pipeline Documentation JavaScript pipeline examples request bmpvieira
Gasket pipeline Documentation Gasket pipeline example request bmpvieira
Dat/Bionode workshop Documentation Online workshop presented at Mozfest 2014 request bmpvieira
ensembl Data access Access to ENSEMBL API request nerdstrike emepyc daviddao
blast-parser Parser Basic Local Alignment Search Tool request greenify
sra Wrappers SRA Toolkit development bmpvieira olgabot mlovci
bwa Wrappers Burrows-Wheeler Aligner development bmpvieira
sam Wrappers Sequence Alignment/Map tools development bmpvieira ekg
bbi Parser BBI (bigWig and bigBed) development bmpvieira dasmoth
obo Parser OBO 1.2 streaming parser development thejmazz
quickgo Data access Acess to EBI QuickGO development thejmazz
ebi Data access Access to EBI API request bmpvieira olgabot mlovci arq5x
semantic Data access Access to semantic web resources request bmpvieira ktym
vcf Parser Variant Call Format parser request bmpvieira
gff Parser General Feature Format parser request bmpvieira
bowtie Wrappers Bowtie aligner request bmpvieira
sge Wrappers Sun Grid Engine request bmpvieira maxogden ekg gawbul mkuzak badryan
blast Wrappers Basic Local Alignment Search Tool request bmpvieira
vsearch Wrappers Search and clustering request bmpvieira
khmer Wrappers k-mer counting & filtering request bmpvieira
rsem Wrappers RNA-Seq by Expectation-Maximization request olgabot
gmap Wrappers Genomic Mapping and Alignment Program request olgabot
star Wrappers Spliced Transcripts Alignment to a Reference request olgabot
go Wrappers Gene ontology request badryan

[1]: Current status of the module

  • production means the module is still in development but has many features complete and is used intensively.
  • development means the module still lacks some features, tests or has some issues.
  • request means the module has been requested, discussed and planned, but is not yet implemented.

[2]: People involved in this module, either through code contribution, ideas or discussion.

Support

If you find a bug please use the issues tracker to report it.
If you need help with this particular module, you can use the respective gitter chat room.
For general help or discussion about the bionode project, you can use the IRC channel #bionode on Freenode.
Bionode is collaborating with BioJS which also has a IRC channel at #biojs.

Contributing

Please see CONTRIBUTING.md for how to contribute to this project.
For a list of contributors, see the file contributors.md.

Contacts

Bruno Vieira <mail@bmpvieira.com> @bmpvieira
Yannick Wurm (yannick.poulet.org) @yannick__

License

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