https://github.com/bioSyntax/bioSyntax

Syntax highlighting for computational biology
https://github.com/bioSyntax/bioSyntax

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: about 2 months ago
JSON representation

Syntax highlighting for computational biology

• Host: GitHub
• URL: https://github.com/bioSyntax/bioSyntax
• Owner: bioSyntax
• License: gpl-3.0
• Created: 2017-12-05T02:25:00.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2023-03-04T03:17:52.000Z (over 1 year ago)
• Last Synced: 2024-04-29T02:10:38.432Z (2 months ago)
• Topics: bam, bioinformatics, computational-biology, fasta, gedit, less, pdb, sublime-text, syntax-highlighting, vcf, vim
• Language: Shell
• Homepage: http://bioSyntax.org
• Size: 2.53 MB
• Stars: 247
• Watchers: 17
• Forks: 30
• Open Issues: 12
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.md

Lists

• Awesome-Bioinformatics - bioSyntax - Syntax Highlighting for Computational Biology file formats (SAM, VCF, GTF, FASTA, PDB, etc...) in vim/less/gedit/sublime. [ [paper-2018](https://pubmed.ncbi.nlm.nih.gov/30134911) | [web](http://www.bioSyntax.org) ] (Data Processing / Command Line Utilities)
• awesome-stars - bioSyntax/bioSyntax - Syntax highlighting for computational biology (Shell)
• Awesome-Bioinformatics-CN - bioSyntax - vim/less/gedit/submie中生物数据格式(SAM, VCF, GTF, FASTA, PDB等)语法高亮 [ [paper-2018](https://pubmed.ncbi.nlm.nih.gov/30134911) | [web](http://www.bioSyntax.org) ] (数据处理 / 命令行工具)

README

        
![bioSyntax Logo](bioSyntax_logo.png)

![Fasta Banner](http://biosyntax.org/images/fa-banner.png)

Syntax highlighting for computational biology to bring you intuitively close to your data.

Support in **vim**, **less**, **sublime3** & **gedit** for `.sam`, `.flagstat`, `.vcf`, `.fasta`, `.fastq`, `.faidx`, `.clustal`, `.pdb`, `.gtf`, `.bed` files & more.

# [bioSyntax.org](http://biosyntax.org/)

### We'd like to know how bioSyntax can be developed to help your workflow. [Tell us what you think! (~5m)](https://goo.gl/forms/YO89fEPw71JpH3Ac2)

## Usage

bioSyntax integrates seamlessly with your text editor, recognizing data-type by the file extension or streamed into `less`.

To gain the most insight from your data, read our brief [bioSyntax Manual](http://bioSyntax.org/man).

## [Download Latest Release](https://www.bioSyntax.org/release)

## [Install](http://bioSyntax.org/install)

## [Screenshots](http://biosyntax.org/screenshots)

`samtools view -h NA19238.bam | sam-less - `

![sam-less](http://biosyntax.org/images/sam-less-small.gif)

*************************************************

### [Collaborate](CONTRIBUTING.md)

Dev Team: [Artem Babaian](https://github.com/ababaian) | [Dylan Aïssi](https://github.com/daissi) | [Anicet Ebou](https://github.com/ebedthan) | [Alyssa Fegen](https://github.com/alyeffy) | [Jeffrey Kam](https://github.com/lazypanda10117) | [Gherman Novakovskiy](https://github.com/fransilvion) | [Li Yao](https://github.com/liyao001) | [Jasper Wong](https://github.com/Jwong684)

Contact us: [info[AT]biosyntax.org](mailto:[email protected])

A [hackseq17](https://www.hackseq.com) Initiative.