1278 Open source projects that are alternatives of or similar to Genomics

Data intensive science for everyone.

A package for designing compact and comprehensive capture probe sets.

UGENE is free open-source cross-platform bioinformatics software

Official code repository for GATK versions 4 and up

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

Analysis pipelines for sequencing data

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

A repository for setting up a RNAseq workflow

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

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

An open source platform for managing and analyzing biomedical big data

Efficient pythonic random access to fasta subsequences

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

Rapid large-scale prokaryote pan genome analysis

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

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

Genomics Extension for SQLite

NGLess: NGS with less work

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

A tool to circularize genome assemblies

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

highly-efficient & lightweight mutation signature matrix aggregation

cython + htslib == fast VCF and BCF processing

Official git repository for Biopython (originally converted from CVS)

Antimicrobial Resistance Identification By Assembly

Collection of scripts for bacterial genomics

Java utilities for Bioinformatics

A fast 23andMe genome text file parser, now superseded by arv

Intuitive local web frontend for the BLAST bioinformatics tool

Scalable genomic data analysis.

Haplotype VCF comparison tools

A package for designing activity-informed nucleic acid diagnostics for viruses.

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A curated list of awesome bioinformatics software.

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

Structural variant toolkit for VCFs

An interactive web tool for quality control of DNA sequencing data

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

Assembling the cause of phenotypes and genotypes from NGS data

annotate a VCF with other VCFs/BEDs/tabixed files

Bayesian genotyper for structural variants

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

Signal-level algorithms for MinION data

A comprehensive tutorial about GWAS and PRS

Plant image analysis using OpenCV

Bioinformatics library for .NET

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

A modern genome browser built with JavaScript and HTML5.

The next version of bwa-mem

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A fast and sensitive gapped read aligner

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

GCP Essentials for Bioinformatics Researchers

Scripts to download genomes from the NCBI FTP servers

C library for high-throughput sequencing data formats

Tools to process and analyze deep sequencing data.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

tools for working with genome variation graphs