Top 274 genomics open source projects

Haplotype VCF comparison tools

JavaScript VisualizationTools

Official git repository for Biopython (originally converted from CVS)

cython + htslib == fast VCF and BCF processing

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

An ultrafast memory-efficient short read aligner

A Java API for high-throughput sequencing data (HTS) formats.

Performant Pythonic GenomicRanges

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

🔬 BEDOPS: high-performance genomic feature operations

SDK for GPU accelerated genome assembly and analysis

Fast large scale matrix visualization for the web.

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Proof-of-concept seq-to-graph mapper and graph generator

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Intuitive local web frontend for the BLAST bioinformatics tool

A powerful open source data warehouse system

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

Chromosome visualization for the web

Deep learning infrastructure for bioinformatics

Ten Quick Tips for Deep Learning in Biology

Reads simulator

Rapid large-scale prokaryote pan genome analysis

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

An open-source toolkit for large-scale genomic analysis

Viral genomics analysis pipelines

Tools to work with variant call format files

structural variant calling and genotyping with existing tools, but, smoothly.

Genomic Data Retrieval with R

A curated list of bioinformatics bench-marking papers and resources.

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

Bayesian haplotype-based mutation calling

nim wrapper for htslib for parsing genomics data files

MISO: An open-source LIMS for NGS sequencing centres

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

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

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

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

A tool to circularize genome assemblies

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

NGLess: NGS with less work

An R package for creating Q-Q and manhattan plots from GWAS results

A cool place to store your Hi-C

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

variant expressions, annotation, and filtering for great good.

Simulate genealogical trees and genomic sequence data using population genetic models

A collection of scripts and notes related to genomics and bioinformatics

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Antimicrobial Resistance Identification By Assembly

AQUAS TF and histone ChIP-seq pipeline

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

Genomics Extension for SQLite

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

Script to automatically create and run IGV snapshot batchscripts

List of tools and resources related to the 10x Genomics GEMCode/Chromium system