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

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

A faster lmm for GWAS. Supports GPU backend.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

ObsPy: A Python Toolbox for seismology/seismological observatories.

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Precision HLA typing from next-generation sequencing data

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

A lightweight, distributed workflow system

Toolkit for preparing genomes for submission to NCBI

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Fast hash function for DNA sequences

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Compute N50/NG50 and auN/auNG

Method to optimally select samples for validation and resequencing

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

💎 Ruby gem to run and orchestrate background jobs with Zenaton Workflow Engine

List of IARC bioinformatics nextflow pipelines

Simple pure Python SAM parser and objects for working with SAM records

Fast and flexible ORF finder

Bystro genetic analysis (annotation, filtering, statistics)

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

Lightweight workflow engine microservice implement BPMN 2.0

Provide R access to the NCI Genomic Data Commons portal.

Fast alignment and preprocessing of chromatin profiles

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

workflow engine activity activiti

Predict plasmids from uncorrected long read data

An open-access bioinformatics text

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Project metadata manager for PEPs in Python

RNASeq pipeline

CMMN engine implementation in dotnet core

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

De novo assembly based variant calling pipeline for Illumina short reads

Earl Grey: A fully automated TE curation and annotation pipeline

Tukio is an event based workflow generator library

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.

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

This library tackles the construction and efficient execution of computational chemistry workflows

Tools for analyzing 10X Genomics data

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Example client programs for Saphetor's VarSome annotation API

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Use this Property Manager CLI to automate Akamai property changes and deployments across many environments.

A high-performance, Pythonic language for bioinformatics

An analysis and visualization platform for 'omics data

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

Distributed workflow server

A light-weight wrapper library around Spotify's Luigi workflow library to make writing scientific workflows more fluent, flexible and modular

A comprehensive tutorial about GWAS and PRS

Function-oriented Make-like declarative workflows for R

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

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

Check Wiki for details

The easiest way to automate your data

Build workflows, activities, BPMN like processes, or state machines with PVM.