Top 704 bioinformatics open source projects

parallel fastq-dump wrapper

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Bayesian haplotype-based mutation calling

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

A comprehensive library for computational molecular biology

nim wrapper for htslib for parsing genomics data files

Fast multi-line FASTA/Q reader in several programming languages

Simple simulation of single-cell RNA sequencing data

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

ECG classification programs based on ML/DL methods

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Code examples of fast and simple k-mer counters for tutorial purposes

Single cell perturbation prediction

A tool to circularize genome assemblies

Application for making ENCODE Blacklists

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

dna2vec: Consistent vector representations of variable-length k-mers

NGLess: NGS with less work

APBS - software for biomolecular electrostatics and solvation

A cool place to store your Hi-C

An efficient FASTQ manipulation suite

Bio4j abstract model and general entry point to the project

UGENE is free open-source cross-platform bioinformatics software

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Python module for average nucleotide identity analyses

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

A Practical and Efficient NCBI Taxonomy Toolkit

SortMeRNA: next-generation sequence filtering and alignment tool

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

A collection of scripts and notes related to genomics and bioinformatics

pymzML - an interface between Python and mzML Mass spectrometry Files

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Demonstrating best practices for bioinformatics command line tools

Antimicrobial Resistance Identification By Assembly

✏️ A versatile DNA sequence optimizer

A DSL for data-driven computational pipelines

GCP Essentials for Bioinformatics Researchers

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Race and ethnicity Imputation from Disease history with Deep LEarning

Bioinformatics library for .NET

Genomics Extension for SQLite

A robust and fast clustering method for amplicon-based studies

MOLGENIS - for scientific data: management, exploration, integration and analysis.

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

A curated list of awesome Bioinformatics libraries and software.

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Post-analysis of immune repertoire sequencing data

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Bioinformatics Workbook repository

Structural variant toolkit for VCFs

Conda recipes for the bioconda channel.