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

# 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.

ncbiData accessAccess to NCBI API (e-utils)
fastaParserFasta parser
seqWranglingSequence transformation (reverse complement, etc) IsmailM
templateDocumentationExample template module
JS pipelineDocumentationJavaScript pipeline examples
Gasket pipelineDocumentationGasket pipeline example
Dat/Bionode workshopDocumentationOnline workshop presented at Mozfest 2014
ensemblData accessAccess to ENSEMBL API
blast-parserParserBasic Local Alignment Search Tool
sraWrappersSRA Toolkit
bwaWrappersBurrows-Wheeler Aligner
samWrappersSequence Alignment/Map tools
bbiParserBBI (bigWig and bigBed)
ebiData accessAccess to EBI API
semanticData accessAccess to semantic web resources
vcfParserVariant Call Format parser
gffParserGeneral Feature Format parser
bowtieWrappersBowtie aligner
sgeWrappersSun Grid Engine badryan
blastWrappersBasic Local Alignment Search Tool
vsearchWrappersSearch and clustering
khmerWrappersk-mer counting & filtering
rsemWrappersRNA-Seq by Expectation-Maximization
gmapWrappersGenomic Mapping and Alignment Program
starWrappersSpliced Transcripts Alignment to a Reference
goWrappersGene ontologybadryan

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

Bruno Vieira <> @bmpvieira
Yannick Wurm ( @yannick__

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