https://github.com/biowasm/biowasm

WebAssembly modules for genomics
https://github.com/biowasm/biowasm

awk bedtools bioinformatics bowtie2 genomics grep javascript jq minimap2 samtools sed seqtk webassembly

Last synced: 6 months ago
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WebAssembly modules for genomics

• Host: GitHub
• URL: https://github.com/biowasm/biowasm
• Owner: biowasm
• License: mit
• Created: 2019-09-07T15:24:26.000Z (about 6 years ago)
• Default Branch: main
• Last Pushed: 2024-11-01T17:51:20.000Z (11 months ago)
• Last Synced: 2024-11-01T18:30:34.577Z (11 months ago)
• Topics: awk, bedtools, bioinformatics, bowtie2, genomics, grep, javascript, jq, minimap2, samtools, sed, seqtk, webassembly
• Language: HTML
• Homepage: https://biowasm.com
• Size: 5.07 MB
• Stars: 217
• Watchers: 10
• Forks: 23
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
![biowasm logo](https://avatars.githubusercontent.com/u/62475458?s=200&v=4)

# biowasm

![Tests](https://github.com/biowasm/biowasm/workflows/Tests/badge.svg)

![Deploy](https://github.com/biowasm/biowasm/workflows/Deploy%20biowasm%20v3/badge.svg)

A repository of genomics tools, compiled from C/C++ to WebAssembly so they can run in a web browser.

## Getting started

* [Documentation](https://biowasm.com/documentation)

* [List of supported packages](https://biowasm.com/cdn)

## Who uses biowasm?    

| Tool | Why biowasm? |

|-|-|

| [sandbox.bio](https://sandbox.bio) | Runs command-line tools in the browser to power interactive tutorials |

| [42basepairs](https://42basepairs.com) | Runs `samtools`, `bedtools`, `bcftools` and other tools to preview genomic files |

| [CZ ID](https://czid.org/) ([repo](https://github.com/chanzuckerberg/czid-web)) | Runs `htsfile` and `seqtk` to identify data issues before file upload |

| [Nanopore](https://bonito.epi2me.io) | Runs `samtools` to generate `.bam` files after basecalling in the browser |

| [ViralWasm](https://niema-lab.github.io/ViralWasm/) ([repo](https://github.com/Niema-Lab/ViralWasm)) | Runs `minimap2` and `ViralConsensus` for viral molecular epidemiology analysis |

| [Datagrok](https://datagrok.ai) ([repo](https://github.com/datagrok-ai/public)) | Runs `kalign` in the browser for multiple-sequence alignment analysis |

| [bedqc](https://quinlan-lab.github.io/bedqc) ([repo](https://github.com/quinlan-lab/bedqc)) | Runs `bedtools` in the browser to validate BED files |

| [Ribbon](https://genomeribbon.com) ([repo](https://github.com/MariaNattestad/Ribbon)) | Runs `samtools` in the browser to parse, estimate coverage and subsample BAM files |

| [fastq.bio](https://www.fastq.bio) ([repo](https://github.com/robertaboukhalil/fastq.bio)) | Runs `fastp` in the browser to evaluate sequencing data quality |

## How it works

| Tool | Description | Link |

|-|-|-|

| biowasm | Recipes for compiling C/C++ genomics tools to WebAssembly | This repo |

| biowasm CDN | Free server hosting pre-compiled tools for use in your apps | [biowasm.com/cdn](https://biowasm.com/cdn) |

| Aioli | Tool for running these modules in a browser, inside WebWorkers | [biowasm/aioli](https://github.com/biowasm/aioli) |

## Logo

* Logo by [tinygraphs](https://www.tinygraphs.com/#?name=biowasm&shape=labs%2Fisogrids%2Fhexa&theme=seascape&numcolors=4#tryitout)

## Contributing

See [CONTRIBUTING.md](https://github.com/biowasm/biowasm/blob/main/CONTRIBUTING.md).