5808 Open source projects that are alternatives of or similar to Galaxy

UGENE is free open-source cross-platform bioinformatics software

Official code repository for GATK versions 4 and up

A collection of scripts and notes related to genomics and bioinformatics

A package for designing compact and comprehensive capture probe sets.

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 repository for setting up a RNAseq workflow

Robust, flexible and resource-efficient pipelines using Go and the commandline

NGLess: NGS with less work

An open source platform for managing and analyzing biomedical big data

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

Java utilities for Bioinformatics

Intuitive local web frontend for the BLAST bioinformatics tool

Collection of scripts for bacterial genomics

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

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Lightweight workflow engine for .NET Standard

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

Robust and efficient workflows using a simple language agnostic approach

Antimicrobial Resistance Identification By Assembly

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

A tool to circularize genome assemblies

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Official git repository for Biopython (originally converted from CVS)

DEPRECIATED! Please use nf-core/tools instead

Rapid large-scale prokaryote pan genome analysis

Machine is a workflow/pipeline library for processing data

Efficient pythonic random access to fasta subsequences

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Genomics Extension for SQLite

An interactive web tool for quality control of DNA sequencing data

Kogito Runtimes - Kogito is a cloud-native business automation technology for building cloud-ready business applications.

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

Tools to process and analyze deep sequencing data.

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

🔬 BEDOPS: high-performance genomic feature operations

BatchFlow helps you conveniently work with random or sequential batches of your data and define data processing and machine learning workflows even for datasets that do not fit into memory.

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

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

Distributed Workflow Engine for Microservices Orchestration

Kogito examples - Kogito is a cloud-native business automation technology for building cloud-ready business applications.

Cuneiform distributed programming language

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

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

Ultrafast sequence typing and gene detection from NGS raw reads

A library to build and execute typed scientific workflows

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

A curated list of awesome bioinformatics software.

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Assembling the cause of phenotypes and genotypes from NGS data

A simplified pipeline for ctDNA sequencing data analysis

A DSL for data-driven computational pipelines

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

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

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