snakemake

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)

python bioinformatics snakemake panel pcr viterbi multiplexpcr tngs

UpdatedFeb 28, 2025
Python

PyPSA /pypsa-eur

Star404

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

snakemake energy energy-system power-systems energy-model energy-systems pypsa energy-system-model

UpdatedMar 18, 2025
Python

maxplanck-ie /snakepipes

Star394

Customizable workflows based on snakemake and python for the analysis of NGS data

workflow rna-seq snakemake ngs hi-c chip-seq atac-seq bisulfite-sequencing

UpdatedMar 18, 2025
Python

metagenome-atlas /atlas

Star384

ATLAS - Three commands to start analyzing your metagenome data

snakemake annotation assembly metagenomics taxonomic-classifications genomic-binning functional-annotation

UpdatedMar 17, 2025
Python

snakemake-workflows /rna-seq-star-deseq2

Star339

RNA-seq workflow using STAR and DESeq2

snakemake deseq2 reproducibility sciworkflows gene-expression-analysis

UpdatedAug 1, 2024
Python

snakemake-workflows /dna-seq-gatk-variant-calling

Star250

This Snakemake pipeline implements the GATK best-practices workflow

snakemake gatk reproducibility sciworkflows genomic-variant-calling

UpdatedJun 8, 2023
Python

franciscozorrilla /metaGEM

Star229

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

bioinformatics snakemake systems-biology computational-biology metagenomics metabolism microbiome metabolic-models flux-balance-analysis microbial-ecology gut-microbiome mags genome-scale-metabolic-model metagenome-assembled-genomes metabolic-modeling

UpdatedJul 27, 2024
Python

gustaveroussy /sopa

Star175

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

snakemake pipeline memory-management generalization spatial-transcriptomics spatialdata multiplexed-imaging spatial-omics

UpdatedMar 17, 2025
Python

sunbeam-labs /sunbeam

Star169

A robust, extensible metagenomics pipeline

snakemake reproducible-research metagenomics

UpdatedAug 15, 2024
Python

snakemake /snakefmt

Star159

The uncompromising Snakemake code formatter

python formatter fmt bioinformatics snakemake code black codeformatter

UpdatedMar 14, 2025
Python

vanheeringen-lab /seq2science

Star156

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.

bioinformatics rna-seq snakemake pipeline reproducible-research ngs bioinformatics-pipeline chip-seq atac-seq workflows fastq sra

UpdatedFeb 5, 2024
Python

snakemake-workflows /docs

Star153

Documentation of the Snakemake-Workflows project

snakemake snakemake-workflows

UpdatedFeb 2, 2022

jdblischak /smk-simple-slurm

Star151

A simple Snakemake profile for Slurm without --cluster-config

bioinformatics snakemake slurm snakemake-profile

UpdatedJun 20, 2024
Shell

Hoohm /dropSeqPipe

Star147

A SingleCell RNASeq pre-processing snakemake workflow

yaml picard snakemake pipeline plot conda multiqc star umi reference-genome drop-seq dropseq scrbseq scrb-seq dropseqtools

UpdatedJan 11, 2023
Python

sequana /sequana

Star146

Sequana: a set of Snakemake NGS pipelines

coverage rna-seq snakemake taxonomy ngs pacbio variant-calling de-novo sequanix

UpdatedFeb 27, 2025
Jupyter Notebook

cbg-ethz /V-pipe

Star135

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

bioinformatics snakemake virus genomics ngs sequencing conda bioinformatics-pipeline hiv sars-cov-2 sarscov2 biohackeu20 biohackcovid20 biohackeu21 biohackeu22

UpdatedMar 13, 2025
Jupyter Notebook

crazyhottommy /pyflow-ChIPseq

Star106

a snakemake pipeline to process ChIP-seq files from GEO or in-house

python snakemake chip-seq

UpdatedApr 17, 2020
Python

moiexpositoalonsolab /grenepipe

Star96

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

snakemake variant-calling population-genetics variant-calls snakemake-workflow pool-sequencing ancient-dna evolve-and-resequence genomic-variant-calling

UpdatedFeb 24, 2025
Python

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