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https://github.com/dissipative/awesome-bio-go

A curated list of Bioinformatics software written in the Go language.
https://github.com/dissipative/awesome-bio-go

List: awesome-bio-go

bioinformatics bioinformatics-pipeline go golang

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A curated list of Bioinformatics software written in the Go language.

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# (Awesome?) List of Bioinformatics Software Written in the Go Language



There are several reasons why there isn't as much software written in Go for bioinformatics. The primary reason is

historical — Languages like Python and R have historically been popular in the bioinformatics community due to their

ease of use, extensive libraries, and strong community support. Many existing bioinformatics tools and workflows are

already written in these languages, making it easier for new projects to build on top of existing solutions.



Despite all the challenges, Go's simplicity, performance, and concurrency support could make it

a viable option for certain bioinformatics applications, especially those that require efficient multi-threading

or that need to be deployed as standalone binaries. As Go continues to grow and gain traction in various industries,

it's possible that we'll see an increase in the number of bioinformatics projects written in the language.



A quick search on the internet, especially on GitHub, has shown me that a lot of work has been done in this direction

in the last decade. Starting from the classical "all-in-one bio package" _biogo_, which seems to have been abandoned in

recent years, several enthusiasts continued to expand the code base and created more and more tools, mainly for

molecular data manipulation.



I want to especially emphasize two developers and researchers: [Wei Shen](http://shenwei.me) from the Institute for

Viral Hepatitis, China and [Brent Pedersen](https://github.com/brentp), a genomicist from the Netherlands —

most of the libs and tools in this list were made by them. I haven't had enough time yet to check all the items on the

list, so I anticipate that it will change (be extended or refined) in the near future.



Feel free to [send a pull request](https://github.com/dissipative/awesome-bio-go/compare),

[open an issue](https://github.com/dissipative/awesome-bio-go/issues/new),

or DM for changes or send me your pieces of code!



See also [awesome-biology](https://github.com/raivivek/awesome-biology) and

[Awesome-Bioinformatics](https://github.com/danielecook/Awesome-Bioinformatics).



## Table of Contents



- [(Awesome?) List of Bioinformatics Software Written in the Go Language](#awesome-list-of-bioinformatics-software-written-in-the-go-language)

  - [Table of Contents](#table-of-contents)

  - [Workflow and Pipeline Management](#workflow-and-pipeline-management)

  - [General Bioinformatics Libraries](#general-bioinformatics-libraries)

  - [Proteomics and Genomics Analysis](#proteomics-and-genomics-analysis)

  - [Sequence Analysis and Manipulation](#sequence-analysis-and-manipulation)

  - [Variant Analysis and Manipulation](#variant-analysis-and-manipulation)

  - [Data Manipulation and Querying](#data-manipulation-and-querying)

  - [DICOM Parsing](#dicom-parsing)

  - [Name and Taxonomy Analysis](#name-and-taxonomy-analysis)

  - [Biochemistry](#biochemistry)

  - [License](#license)



## Workflow and Pipeline Management



- [SciPipe](https://github.com/scipipe/scipipe) — Workflow library embedded in the Go programming language,

focusing on complex workflow constructs, compiling to a single binary, and providing powerful file naming and

comprehensive audit reports for every output.

[ [paper-2019](https://pubmed.ncbi.nlm.nih.gov/31029061/) | [web](https://scipipe.org/) ]

- [Reflow](https://github.com/grailbio/reflow) — A language and runtime for distributed, incremental

data processing in the cloud



## General Bioinformatics Libraries



- [bíogo](https://github.com/biogo/biogo) — Bioinformatics library for Go. (Updated 2 years ago!)

- [Gonetics](https://github.com/pbenner/gonetics) — Go/Golang Bioinformatics Library. (Updated 2 years ago!)

- [Grail Bioinformatics tools](https://github.com/grailbio/bio) — Bioinformatic infrastructure libraries.

(Updated 3 years ago!)



## Proteomics and Genomics Analysis



- [Philosopher](https://github.com/Nesvilab/philosopher) — Complete toolkit for shotgun proteomics data analysis.

- [samql](https://github.com/maragkakislab/samql) — SQL-like query language for the SAM/BAM file format.



## Sequence Analysis and Manipulation



- [SeqKit](https://github.com/shenwei356/seqkit) — Cross-platform and ultrafast toolkit for FASTA/Q file manipulation.

- [KMCP](https://github.com/shenwei356/kmcp) — Accurate metagenomic profiling and fast large-scale sequence/genome

searching. [ [paper](https://doi.org/10.1093/bioinformatics/btac845) ]

- [bio](https://github.com/shenwei356/bio) — Lightweight and high-performance bioinformatics package in Golang.

- [unikmer](https://github.com/shenwei356/unikmer) — Toolkit for k-mers with taxonomic information.

- [bwt](https://github.com/shenwei356/bwt) — Burrows-Wheeler Transform and FM-index in Golang.

- [gTaxon](https://github.com/shenwei356/gtaxon) — Fast cross-platform NCBI taxonomy data querying tool with

cmd client and REST API server.

- [Gotranseq](https://github.com/feliixx/gotranseq) — Convert nucleic sequence to protein sequence.

- [spexs2](https://github.com/egonelbre/spexs2) — An exhaustive sequence pattern search tool



## Variant Analysis and Manipulation



- [smoove](https://github.com/brentp/smoove) — Structural variant calling and genotyping with existing tools,

but smoothly.

- [vcfanno](https://github.com/brentp/vcfanno) — Annotate a VCF with other VCFs/BEDs/tabixed files.

[ [paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5) ]

- [vcfgo](https://github.com/brentp/vcfgo) — Golang library to read, write, and manipulate files in the variant

call format.

- [goleft](https://github.com/brentp/goleft) — Collection of bioinformatics tools distributed under the MIT license

in a single static binary.

- [excord](https://github.com/brentp/excord) — Extract SV signal from a BAM.

- [bcf](https://github.com/brentp/bcf) — BCF parsing in Golang.



## Data Manipulation and Querying



- [taxonkit](https://github.com/shenwei356/taxonkit) — Practical and efficient NCBI Taxonomy Toolkit,

supports creating NCBI-style taxdump files.

- [bget](https://github.com/shenwei356/bget) — Portable command-line tool to query bioinformatics APIs, data,

databases, and files.

- [countminsketch](https://github.com/shenwei356/countminsketch) — Implementation of Count-Min Sketch in Golang.

- [csvtk](https://github.com/shenwei356/csvtk) — Cross-platform, efficient, and practical CSV/TSV toolkit in Golang.



## DICOM Parsing



- [go-dicom](https://github.com/grailbio/go-dicom) — DICOM parser for Golang.



## Name and Taxonomy Analysis



- [GNfinder](https://github.com/gnames/gnfinder) — finds scientific names in UTF8 texts, PDF files,

MS Word/Excel documents, URLs, etc.



## Biochemistry



- [goChem](https://github.com/rmera/gochem) — A library for Computational Chemistry in the Go programming language



## License



[![CC0](https://mirrors.creativecommons.org/presskit/buttons/88x31/svg/cc-zero.svg)](https://creativecommons.org/publicdomain/zero/1.0)