89 Open Source Bioinformatics Pipeline Software Projects

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

A language and runtime for distributed, incremental data processing in the cloud

Analysis Pipeline for Single Cell ATAC-seq

Rapid large-scale prokaryote pan genome analysis

ATAC-seq and DNase-seq processing pipeline

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

Finds SNP sites from a multi-FASTA alignment file

A tool to circularize genome assemblies

NGLess: NGS with less work

Package for fetching metadata and downloading data from SRA/ENA/GEO

Antimicrobial Resistance Identification By Assembly

GCP Essentials for Bioinformatics Researchers

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

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

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

A modular annotation tool for genomic variants

Infectious Disease Sequencing Platform

Cluster single cells and analyze cell clade relationships with colorful visualizations.

A bioinformatics pipeline to analyze mtDNA from NGS data

A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)

Improve the quality of a denovo assembly by scaffolding and gap filling

de novo virus assembler of Illumina paired reads

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

A collection of reusable WDL tasks. Category:Other

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

My daily notebook on bioinformatic data analysis and machine learning

Bystro genetic analysis (annotation, filtering, statistics)

High-throughput gene to knowledge mapping through massive integration of public sequencing data.

Python toolkit for building restartable pipelines

Bioinformatics Ketrew Pipelines

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

Predict plasmids from uncorrected long read data

A novel pipeline framework to accelerate bioinformatics analysis

<<------ Use SnapATAC!!

Assembling the cause of phenotypes and genotypes from NGS data

Phigaro is a scalable command-line tool for predicting phages and prophages

novoBreak: local assembly for breakpoint detection in cancer genomes

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Submit functions and shell scripts to torque and slurm clusters or local machines using python.

GREIN : GEO RNA-seq Experiments Interactive Navigator

DEPRECIATED! Please use nf-core/tools instead

Bioinformatics curated workflows that use Biocontainers tools

A comprehensive pipeline for short read metagenomic data

ASAP : Automated Single-cell Analysis Pipeline

An opinionated Cromwell orchestration manager.

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

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

ConsensusTME Gene Sets and R Script

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

Sentieon DNAseq

Multilocus sequence typing by blast using the schemes from PubMLST

Real-time species-typing visualisation for nanopore data.

Order and orientation of complete bacterial genomes

:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

A job submitter for Portable Encapsulated Projects

Workflow management system for the automated and distributed analysis of large-scale experimental data.

Graphical GUI for Docker (Bioconductor, R, Cytoscape, NetworkBMA)

Snakemake profile for running jobs on an LSF cluster

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

A suite of unique bioinformatics tools for the brave explorer.

Genotype Imputation Pipeline for H3Africa

A set of tools to analyse the output from TraDIS analyses

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

A fully automated gene annotator from RNA-Seq expression data

Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.

Build and maintain multiple custom conda environments all in once place.

From annotated genomes to metabolic screening in large scale microbiotas

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Ploidy agnostic phasing pipeline and algorithm

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

A pipeline for high-quality bacterial genome construction using ONT sequencing

A library for deploying App on deepchain.bio

Scripts and procedures for detecting positively selected genes and codons in primates

Full-Length RNA Analysis pipeline developted by BGI RD group.

Distribution of TEs and their relationship to genes in host genome

Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)

Explore biomolecular pathways in Reactome from the command-line or a Python script

HemTools: a collection of NGS pipelines and bioinformatic analyses

Generate the UMI count matrix from CEL-Seq2 sequencing data

Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads

This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.

Mobile Genetic Elements Retrieving Tool

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.