bionode

About

Bionode.io is an Open Source community building highly reusable code and tools for bioinformatics by leveraging the Node.JS ecosystem.

We want to process big genomic data using Node.JS Streams.

We welcome all kinds of contributions at all levels of experience, either code, knowledge, questions or suggestions.

Examples

# Download human genome
$ bionode-ncbi download assembly human
# Download all Sequence Read Archives for arthropoda and extract a fastq for each
$ bionode-ncbi download sra arthropoda | bionode-sra fastq-dump
# Parse sequences in a fasta file into one JSON object per line, collect the ones that match chr11
$ cat genome.fasta | bionode-fasta | grep chr11 | bionode-fasta --write
# Search pubmed for ten retracted papers and use jq to view the paper's title
$ bionode-ncbi search -l 10 pubmed "\"Retracted Publication\"" | jq '.title'
# Search pubmed for papers with the word 'Cancer' in the title
$ bionode-ncbi search pubmed 'Title:Cancer'
Try them online at
try.bionode.io

Features

Scalable

Streams are everywhere in bionode. This avoids storing intermediate data on disk or run out of memory. Building complex but reproducible pipelines is also easier with Streams

Universal

Bionode runs on every platform that supports Node.js and in browsers. Along with a JavaScript API, bionode provides a CLI interface for better interactivity, and integration with other tools and languages (e.g., R, Ruby, Python)

Modular

Every tool tries to do just one thing well and work independently. This gives more flexibility when building pipelines and more resolution for tracking versions and changes.

Team