A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
- Bds - Scripting language for data pipelines.
- Bpipe - Tool for running and managing bioinformatics pipelines.
- Cluster flow - A command-line pipeline tool which uses common cluster managers to run bioinformatics analysis pipelines.
- Compss - Programming model for distributed infrastructures.
- Conan2 - Light-weight workflow management application.
- Cosmos - Python library for massively parallel workflows.
- Luigi - Luigi is a Python module that helps you build complex pipelines of batch jobs.
- Makeflow - Makeflow is a workflow engine for executing large complex workflows on clusters.
- Nextflow - Flow-based computational toolkit for reproducibile and scalable bioinformatics pipelines.
- OpenGE - Accelerated framework for manipulating and interpreting high-throughput sequencing data
- PipEngine Ruby based launcher for complex biological pipelines.
- Rmake - A wrapper for the creation of Makefiles, enabling massive parallelization.
- Rubra - Pipeline system for bioinformatics workflows.
- Ruffus - Computation Pipeline library for Python.
- Scoop - Scalable COncurrent Operations in Python.
- Snakemake - Tool for running and managing bioinformatics pipelines.
- Swift - Fast easy parallel scripting - on multicores, clusters, clouds and supercomputers.
- Yap - Extensible parallel framework, written in Python using OpenMPI libraries.
- WorldMake - Easy Collaborative Reproducible Computing.
- Biokepler - Bioinformatics Scientific Workflow for Distributed Analysis of Large-Scale Biological Data.
- Chipster - Open source platform for data analysis.
- Galaxy - Web-based platform for biomedical research.
- Pathomx - Interactive data workflows built on Python.
- Yabi - Online research environment for grid, HPC and cloud computing.
- Taverna - Domain independent workflow system.
- Bcbio-nextgen - Validated and scalable variant calling and RNA-seq analysis.
- Piper - A pipeline built on top of GATK Queue.
- SparkSeq - A tool for the interactive genomic data analysis with nucleotide precision.