1398 Open source projects that are alternatives of or similar to Rnaseq Workflow

Data intensive science for everyone.

UGENE is free open-source cross-platform bioinformatics software

A collection of scripts and notes related to genomics and bioinformatics

Official code repository for GATK versions 4 and up

A package for designing compact and comprehensive capture probe sets.

Robust and efficient workflows using a simple language agnostic approach

Analysis pipelines for sequencing data

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

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

DEPRECIATED! Please use nf-core/tools instead

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

A library to build and execute typed scientific workflows

An analysis and visualization platform for 'omics data

An open source platform for managing and analyzing biomedical big data

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

A cross-platform command-line tool for executing jobs in parallel

Java utilities for Bioinformatics

Pipeline is a package to build multi-staged concurrent workflows with a centralized logging output.

Workflow Description Language - Specification and Implementations

Data and analysis for the Splatter paper

highly-efficient & lightweight mutation signature matrix aggregation

🍴 Web applications made easy. Since 2011.

NLP pipeline software using common workflow language

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

A python-based isomiR quantification and analysis pipeline

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

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

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

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

Function-oriented Make-like declarative workflows for R

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

Signal-level algorithms for MinION data

Plant image analysis using OpenCV

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.

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.

🌈Scaffold genome sequence assemblies using linked read sequencing data

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

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

An interactive web tool for quality control of DNA sequencing data

Snakemake-based workflow for detecting structural variants in WGS data

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

A simplified pipeline for ctDNA sequencing data analysis

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

A library for generating an interactive SVG visualization of CWL workflows

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

Example workflows for the drake R package

Structural variant toolkit for VCFs

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

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

Machine is a workflow/pipeline library for processing data

Genomics Extension for SQLite

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.

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Antimicrobial Resistance Identification By Assembly

NGLess: NGS with less work

A tool to circularize genome assemblies

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

RNASeq pipeline

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.

contains handy groovy workflow-libs scripts