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BioSharp is a pure and test-driven .NET library for use in bioinformatics and related fields.



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.NET Bio

  •    DotNet

.Net Bio is a language-neutral bioinformatics toolkit built using the Microsoft 4.5 .NET Framework to help developers, researchers, and scientists.

BOW - Bioinformatics On Windows


A group of tools run on Windows for Bioinformatics. Include ported tools from Linux (e.g. BWA, SAMTOOLS), and later original Windows applications.

bionode - Modular and universal bioinformatics

  •    Javascript

To use bionode as a command line tool, you can install it globally with -g. Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the node_modules directory by doing the same command without -g.

seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

  •    Go

FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This project describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OS X, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.


  •    Java

Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.

scikit-bio - scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics

  •    Python

scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. To view scikit-bio's documentation, visit

bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

  •    C

Note: minimap2 has replaced BWA-MEM for PacBio and Nanopore read alignment. It retains all major BWA-MEM features, but is ~50 times as fast, more versatile, more accurate and produces better base-level alignment. BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, is generally recommended as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

csvtk - A cross-platform, efficient and practical CSV/TSV toolkit in Golang

  •    Go

Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data sicence. People usually use spreadsheet softwares like MS Excel to do process table data. However it's all by clicking and typing, which is not automatically and time-consuming to repeat, especially when we want to apply similar operations with different datasets or purposes.

CLCB - Common Lisp Computational Biology


The Common Lisp Computational Biology (CLCB) package is intended to be a comprehensive, flexible and easy to use library for bioinformatics and computational biology.


  •    DotNet

The Bio++/CLR project represents the porting of Bio++ version 1.9 to C#.

Java Evolutionary Biology Library

  •    Java

A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.

Mitrion-C Open Bio Project


The purpose of Mitrion-C Open Bio Project is to develop FPGA accelerated bioinformatics applications for the Mitrion Virtual Processor. The first accelerated application is NCBI BLAST.

BioJava - Java Framework for Processing Biological Data

  •    Java

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

rust-bio - This library provides implementations of many algorithms and data structures that are useful for bioinformatics

  •    Rust

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration. Please see the homepage for examples and documentation.


  •    CSharp

BioSharp is an open source framework for processing biological data, based on BioJava.


  •    Java

This is a small and easy-to-use bio informatics tool for rookie and expert biologists to split files which contain sequences (these files can contain nucleotide, genome or protein sequences) into individual ' .fasta ' files.

freebayes - Bayesian haplotype-based genetic polymorphism discovery and genotyping.

  •    C++

FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. FreeBayes uses short-read alignments (BAM files with Phred+33 encoded quality scores, now standard) for any number of individuals from a population and a reference genome (in FASTA format) to determine the most-likely combination of genotypes for the population at each position in the reference. It reports positions which it finds putatively polymorphic in variant call file (VCF) format. It can also use an input set of variants (VCF) as a source of prior information, and a copy number variant map (BED) to define non-uniform ploidy variation across the samples under analysis.

bioawk - BWK awk modified for biological data

  •    C

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk. The original awk requires a YACC-compatible parser generator (e.g. Byacc or Bison). Bioawk further depends on zlib so as to work with gzip'd files.

Bio Workflow Engine

  •    DotNet

BioWF is a scientific workflow project which allows for easy construction of bioinformatic applications through drag/drop style creation.

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