Top 274 genomics open source projects

Pan-genome wide association studies

Bayesian genotyper for structural variants

A fast whole-genome aligner based on de Bruijn graphs

An interactive web tool for quality control of DNA sequencing data

Flexible genotype query among 30,000+ samples whole-genome

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

A friendly next-generation interface for Genomic data discovery powered by InterMine

A collaboratively written review paper on deep learning, genomics, and precision medicine

Model and predict short DNA sequence features with neural networks

Development repository for the Bioconductor package 'mixOmics '

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Framework for building fast genomics web tools with WebAssembly and WebWorkers

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Analysis pipelines for sequencing data

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Official code repository for GATK versions 4 and up

RADseq Data Exploration, Manipulation and Visualization using R

A list of web-based interactive biological data visualizations.

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A collection of publications on comparison of high-throughput sequencing technologies.

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

Efficient variant-call data storage and retrieval library using the TileDB storage library.

A Suite of Packages for Analysis of Big Genomic Data

Data intensive science for everyone.

tools for working with genome variation graphs

Scalable genomic data analysis.

Python and C++ code for reading and writing genomics data.

Scripts to download genomes from the NCBI FTP servers

Tools to process and analyze deep sequencing data.

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Python library to handle Gene Ontology (GO) terms

C++ library and cmdline tools for parsing and manipulating VCF files

The next version of bwa-mem

Python library to facilitate genome assembly, annotation, and comparative genomics

A modern genome browser built with JavaScript and HTML5.

A fast and sensitive gapped read aligner

Ultra-fast and memory-efficient (meta-)genome assembler

Java utilities for Bioinformatics

Efficient pythonic random access to fasta subsequences

A comprehensive tutorial about GWAS and PRS

An open source platform for managing and analyzing biomedical big data

A high-performance, Pythonic language for bioinformatics

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

A React web application to query and share any PostgreSQL database.

annotate a VCF with other VCFs/BEDs/tabixed files

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Fast genome-wide functional annotation through orthology assignment

PHANOTATE: a tool to annotate phage genomes.

Example client programs for Saphetor's VarSome annotation API

Detection of NCLDV signatures in 'omic data

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

De novo genome assembly and multisample variant calling

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

De novo assembly based variant calling pipeline for Illumina short reads

BACNET is a Java based platform to develop website for multi-omics analysis

Earl Grey: A fully automated TE curation and annotation pipeline

A fast 23andMe genome text file parser, now superseded by arv