bionode

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


bionode.io

# bionode > Modular and universal bioinformatics


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

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.

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.

The following are modules available/planned for Bionode.

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

[1]: Current status of the module

  • means the module is still in development but has many features complete and is used intensively.
  • means the module still lacks some features, tests or has some issues.
  • 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.

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.

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

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

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