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The Top 23 Snakemake Open Source Projects

Open source projects categorized as Snakemake
Categories > Snakemake
Snakemake ⭐ 2,030
This is the development home of the workflow management system Snakemake. For general information, see
dependent packages 115total releases 284most recent commit 3 months agopypi snakemake} Downloads
Rna Seq Analysis ⭐ 614
RNAseq analysis notes from Ming Tang
most recent commit 2 years ago
Snakepipes ⭐ 359
Customizable workflows based on snakemake and python for the analysis of NGS data
most recent commit 3 months ago
Atlas ⭐ 332
ATLAS - Three commands to start analyzing your metagenome data
total releases 25most recent commit 3 months ago
Rna Seq Star Deseq2 ⭐ 282
RNA-seq workflow using STAR and DESeq2
most recent commit 5 months ago
Pypsa Eur ⭐ 278
PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System
most recent commit 10 days ago
Sunbeam ⭐ 157
A robust, extensible metagenomics pipeline
most recent commit 3 months ago
Metagem ⭐ 155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
most recent commit 4 months ago
Dna Seq Gatk Variant Calling ⭐ 138
This Snakemake pipeline implements the GATK best-practices workflow
most recent commit 3 years ago
Sequana ⭐ 136
Sequana: a set of Snakemake NGS pipelines
dependent packages 8total releases 90most recent commit 3 months agopypi sequana} Downloads
Dropseqpipe ⭐ 134
A SingleCell RNASeq pre-processing snakemake workflow
total releases 2most recent commit a year 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
Snakefmt ⭐ 131
The uncompromising Snakemake code formatter
dependent packages 2total releases 29most recent commit 3 months agopypi snakefmt} Downloads
Multiprime ⭐ 123
multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))
most recent commit 3 months ago
Docs ⭐ 120
Documentation of the Snakemake-Workflows project
most recent commit 2 years ago
V Pipe ⭐ 119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
most recent commit 4 months ago
Smk Simple Slurm ⭐ 80
A simple Snakemake profile for Slurm without --cluster-config
most recent commit a year ago
Dna Seq Varlociraptor ⭐ 76
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
most recent commit 4 months ago
Grenepipe ⭐ 75
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
most recent commit 4 months ago
Tibanna ⭐ 68
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
dependent packages 1total releases 280most recent commit 3 months agopypi tibanna} Downloads
Rna Seq Kallisto Sleuth ⭐ 63
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
most recent commit 3 months ago
Panoptes ⭐ 59
Monitor computational workflows in real time
total releases 5most recent commit 4 months ago
Snakefiles ⭐ 58
🐍 Snakefiles for common RNA-seq data analysis workflows.
most recent commit 7 years ago
The 5 Most Depended On Snakemake Open Source Projects
Snakemake ⭐ 2,030
This is the development home of the workflow management system Snakemake. For general information, see
dependent packages 115total releases 284latest release September 18, 2023most recent commit 3 months agopypi snakemake} Downloads
Sequana ⭐ 136
Sequana: a set of Snakemake NGS pipelines
dependent packages 8total releases 90latest release December 06, 2023most recent commit 3 months agopypi sequana} Downloads
Snakefmt ⭐ 131
The uncompromising Snakemake code formatter
dependent packages 2total releases 29latest release October 05, 2023most recent commit 3 months agopypi snakefmt} Downloads
Pytest Workflow ⭐ 52
Configure workflow/pipeline tests using yaml files.
dependent packages 1total releases 18latest release January 13, 2023most recent commit 8 months agopypi pytest-workflow} Downloads
The 10 Latest Releases In Snakemake Open Source Projects
Sequana ⭐ 136
Sequana: a set of Snakemake NGS pipelines
dependent packages 8total releases 90latest release December 06, 2023most recent commit 3 months agopypi sequana} Downloads
Monsda ⭐ 10
MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis
total releases 14latest release November 26, 2023most recent commit 5 months ago
Snakedoc ⭐ 9
A Sphinx extension for Snakemake workflows
total releases 4latest release November 21, 2023most recent commit 5 months ago
Snakefmt ⭐ 131
The uncompromising Snakemake code formatter
dependent packages 2total releases 29latest release October 05, 2023most recent commit 3 months agopypi snakefmt} Downloads
Snakemake ⭐ 2,030
This is the development home of the workflow management system Snakemake. For general information, see
dependent packages 115total releases 284latest release September 18, 2023most recent commit 3 months agopypi snakemake} Downloads
Panoptes ⭐ 59
Monitor computational workflows in real time
total releases 5latest release August 07, 2023most recent commit 4 months ago
Hecatomb ⭐ 36
hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
total releases 1latest release March 30, 2023most recent commit 5 months ago
Pytest Workflow ⭐ 52
Configure workflow/pipeline tests using yaml files.
dependent packages 1total releases 18latest release January 13, 2023most recent commit 8 months agopypi pytest-workflow} Downloads
Dentist ⭐ 44
Close assembly gaps using long-reads at high accuracy.
total releases 13latest release September 14, 2022most recent commit 10 months ago
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