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The Top 23 Bioinformatics Pipeline Open Source Projects

Open source projects categorized as Bioinformatics Pipeline
Categories > Bioinformatics Pipeline
Scipipe ⭐ 1,010
Robust, flexible and resource-efficient pipelines using Go and the commandline
total releases 47most recent commit 9 months ago
Reflow ⭐ 946
A language and runtime for distributed, incremental data processing in the cloud
total releases 2most recent commit 6 months ago
Bacalhau ⭐ 555
Compute over Data framework for public, transparent, and optionally verifiable computation
dependent packages 3total releases 20most recent commit 3 months agopypi bacalhau-sdk} Downloads
Pysradb ⭐ 269
Package for fetching metadata and downloading data from SRA/ENA/GEO
dependent packages 7total releases 38most recent commit 7 months agopypi pysradb} Downloads
Snapatac ⭐ 227
Analysis Pipeline for Single Cell ATAC-seq
most recent commit 2 years ago
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83most recent commit 2 years ago
Circlator ⭐ 193
A tool to circularize genome assemblies
total releases 33most recent commit 8 months ago
Artemis ⭐ 191
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
most recent commit a year ago
Gcp For Bioinformatics ⭐ 178
GCP for Bioinformatics Researchers
most recent commit 3 months ago
Snp Sites ⭐ 173
Finds SNP sites from a multi-FASTA alignment file
most recent commit 3 years ago
Ngless ⭐ 141
NGLess: NGS with less work
total releases 5most recent commit a year ago
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54most recent commit a year agopypi ariba} Downloads
Atac_dnase_pipelines ⭐ 135
ATAC-seq and DNase-seq processing pipeline
most recent commit 5 years ago
Gubbins ⭐ 133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
most recent commit 5 months ago
Seq2science ⭐ 132
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.
most recent commit 5 months ago
Toga ⭐ 120
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.
most recent commit 3 months ago
V Pipe ⭐ 119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
most recent commit 4 months ago
Methylpy ⭐ 116
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
most recent commit a year ago
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43most recent commit 3 months ago
Open Cravat ⭐ 98
A modular annotation tool for genomic variants
most recent commit 6 months ago
Too Many Cells ⭐ 95
Cluster single cells and analyze cell clade relationships with colorful visualizations.
total releases 30most recent commit 4 months ago
Ilus ⭐ 89
A handy variant calling pipeline generator for whole-genome 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.
total releases 13most recent commit 4 months ago
Wholegenomesequencing ⭐ 86
Whole Genome Sequencing analysis, WGS analysis
most recent commit 9 months ago
The 7 Most Depended On Bioinformatics Pipeline Open Source Projects
Pysradb ⭐ 269
Package for fetching metadata and downloading data from SRA/ENA/GEO
dependent packages 7total releases 38latest release September 17, 2023most recent commit 7 months agopypi pysradb} Downloads
Bacalhau ⭐ 555
Compute over Data framework for public, transparent, and optionally verifiable computation
dependent packages 3total releases 20latest release October 09, 2023most recent commit 3 months agopypi bacalhau-sdk} Downloads
Pypiper ⭐ 42
Python toolkit for building restartable pipelines
dependent packages 3total releases 22latest release November 15, 2023most recent commit 4 months agopypi piper} Downloads
Runjob ⭐ 9
runjob is a program for managing a group of related jobs running on a compute cluster
dependent packages 2total releases 39latest release November 01, 2023most recent commit 3 months agopypi runjob} Downloads
R2g ⭐ 49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
dependent packages 1total releases 6latest release November 23, 2020most recent commit 3 years agopypi r2g} Downloads
Hicstuff ⭐ 17
Simple library/pipeline to generate and handle Hi-C data.
dependent packages 1total releases 128latest release September 06, 2023most recent commit 3 years agopypi hicstuff} Downloads
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54latest release September 07, 2020most recent commit a year agopypi ariba} Downloads
The 10 Latest Releases In Bioinformatics Pipeline Open Source Projects
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43latest release November 22, 2023most recent commit 3 months ago
Pypiper ⭐ 42
Python toolkit for building restartable pipelines
dependent packages 3total releases 22latest release November 15, 2023most recent commit 4 months agopypi piper} Downloads
Runjob ⭐ 9
runjob is a program for managing a group of related jobs running on a compute cluster
dependent packages 2total releases 39latest release November 01, 2023most recent commit 3 months agopypi runjob} Downloads
Bacalhau ⭐ 555
Compute over Data framework for public, transparent, and optionally verifiable computation
dependent packages 3total releases 20latest release October 09, 2023most recent commit 3 months agopypi bacalhau-sdk} Downloads
Pysradb ⭐ 269
Package for fetching metadata and downloading data from SRA/ENA/GEO
dependent packages 7total releases 38latest release September 17, 2023most recent commit 7 months agopypi pysradb} Downloads
Hicstuff ⭐ 17
Simple library/pipeline to generate and handle Hi-C data.
dependent packages 1total releases 128latest release September 06, 2023most recent commit 3 years agopypi hicstuff} Downloads
Too Many Cells ⭐ 95
Cluster single cells and analyze cell clade relationships with colorful visualizations.
total releases 30latest release October 06, 2022most recent commit 4 months ago
Metage2metabo ⭐ 42
From annotated genomes to metabolic screening in large scale microbiotas
total releases 33latest release September 26, 2022most recent commit 3 months ago
Ngless ⭐ 141
NGLess: NGS with less work
total releases 5latest release September 19, 2022most recent commit a year ago
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