Top workflows by stars

snakemake-workflows

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

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Updated: 2024-09-13 Release: v2.1.2formatting: passedlinting: passed

321 stars

11 watchers

snakemake-workflows

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

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Updated: 2023-06-29 Release: v2.1.1formatting: failedlinting: passed

207 stars

9 watchers

franciscozorrilla

metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and pred…

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Updated: 2024-09-19 Release: v1.0.5formatting: failedlinting: failed

189 stars

5 watchers

cbg-ethz

V-pipe

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

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Updated: 2025-04-25 Release: v3.0.0.pre1formatting: passedlinting: failed

136 stars

9 watchers

moiexpositoalonsolab

grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads,…

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Updated: 2025-03-27 Release: v0.15.0formatting: passedlinting: failed

96 stars

3 watchers

mrvollger

StainedGlass

Make colorful identity heatmaps of genomic sequence

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Updated: 2024-07-16 Release: v0.6formatting: passedlinting: passed

93 stars

5 watchers

snakemake-workflows

dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/nor…

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Updated: 2025-04-16 Release: v5.16.0formatting: failedlinting: failed

86 stars

7 watchers

GooglingTheCancerGenome

sv-callers

Snakemake-based workflow for detecting structural variants in genomic data

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Updated: 2025-02-14 Release: v1.2.2formatting: failedlinting: failed

79 stars

4 watchers

snakemake-workflows

rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

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Updated: 2025-04-24 Release: v2.11.0formatting: failedlinting: passed

68 stars

4 watchers

epigen

atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Mo…

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Updated: 2024-12-01 Release: v2.0.0formatting: failedlinting: failed

48 stars

3 watchers

zavolanlab

zarp

The Zavolab Automated RNA-seq Pipeline

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Updated: 2025-04-22 Release: v1.0.0formatting: passedlinting: passed

35 stars

6 watchers

epigen

enrichment_analysis

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment …

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Updated: 2024-12-19 Release: v2.0.0formatting: failedlinting: failed

32 stars

2 watchers

sneuensc

mapache

mapping pipeline for ancient DNA

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Updated: 2024-10-28 Release: v0.3.0formatting: failedlinting: failed

26 stars

5 watchers

akcorut

kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

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Updated: 2024-06-11 Release: v1.3.0formatting: failedlinting: failed

26 stars

3 watchers

epigen

unsupervised_analysis

A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensio…

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Updated: 2025-03-04 Release: v3.0.1formatting: failedlinting: failed

24 stars

4 watchers