greenstick / bionode

Modular and universal bioinformatics

bionode.io

# bionode > Modular and universal bioinformatics

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)
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.

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 <[email protected]> @bmpvieira
Yannick Wurm (yannick.poulet.org) @yannick__

License

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