1810 Open source projects that are alternatives of or similar to Sarek

A DSL for data-driven computational pipelines

Data intensive science for everyone.

Example workflows for the drake R package

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

Robust and efficient workflows using a simple language agnostic approach

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

DEPRECIATED! Please use nf-core/tools instead

Analysis pipelines for sequencing data

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JavaScript VisualizationTools

A repository for setting up a RNAseq workflow

An open source platform for managing and analyzing biomedical big data

VisTrails is an open-source data analysis and visualization tool. It provides a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the computational processes that derive these products and their executions.

A library to build and execute typed scientific workflows

An R-focused pipeline toolkit for reproducibility and high-performance computing

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

A collection of scripts and notes related to genomics and bioinformatics

🔬 BEDOPS: high-performance genomic feature operations

Function-oriented Make-like declarative workflows for R

Workflow Description Language - Specification and Implementations

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

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

Curated set of transformers that make your work with steppy faster and more effective 🔭

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A versatile pairwise aligner for genomic and spliced nucleotide sequences

Code examples of fast and simple k-mer counters for tutorial purposes

Scalable genomic data analysis.

NGLess: NGS with less work

System for containerized apps management. From build to scaling.

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

Snakemake-based workflow for detecting structural variants in WGS data

contains handy groovy workflow-libs scripts

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

Official code repository for GATK versions 4 and up

Source code for the CERN Analysis Preservation portal

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

A library for generating an interactive SVG visualization of CWL workflows

Model and predict short DNA sequence features with neural networks

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

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

NLP pipeline software using common workflow language

ATAC-seq peak-calling, QC and differential analysis pipeline

A cool place to store your Hi-C

Bayesian genotyper for structural variants

Machine is a workflow/pipeline library for processing data

Lightweight, Python library for fast and reproducible experimentation 🔬

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

A fast whole-genome aligner based on de Bruijn graphs

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

A tool to circularize genome assemblies

Genomics Extension for SQLite

Bioinformatics library for .NET

An interactive web tool for quality control of DNA sequencing data

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Bitnami Docker Image for Apache Airflow

GCP Essentials for Bioinformatics Researchers

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Mutlitenancy for dotnet applications