Snakemake-Workflows

All

30 repositories

read-alignment-pangenome
Public
Standardized snakemake workflow for aligning sequencing reads to a pangenome.
Python
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MIT License
•1•0•0•2•Updated Mar 20, 2026Mar 20, 2026
dna-seq-varlociraptor
Public
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) …
snakemake reproducibility sciworkflows
snakemake reproducibility sciworkflows varlociraptor genomic-variant-calling
Python
•
MIT License
•47•89•9•22•Updated Mar 19, 2026Mar 19, 2026
dna-seq-benchmark
Public
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
Python
•
MIT License
•3•13•9•5•Updated Mar 19, 2026Mar 19, 2026
rna-seq-kallisto-sleuth
Public
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
rna-seq snakemake reproducibility
rna-seq snakemake reproducibility kallisto differential-expression sleuth sciworkflows
Python
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MIT License
•46•68•7•6•Updated Mar 19, 2026Mar 19, 2026
dna-seq-mtb
Public
A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards
Python
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MIT License
•2•4•0•2•Updated Mar 18, 2026Mar 18, 2026
rna-longseq-de-isoform
Public
long read differential expression analysis and splice variant analysis
gene-annotation differential-expression isoform-quantification
gene-annotation differential-expression isoform-quantification
Python
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MIT License
•1•3•2•1•Updated Mar 4, 2026Mar 4, 2026
cellranger-multi
Public
A Snakemake workflow for preprocessing single cell RNAseq (scRNA-seq) data with `cellranger multi` (Cell Ranger licensing requires a manual download of the soft…
Python
•
MIT License
•0•0•0•2•Updated Feb 25, 2026Feb 25, 2026
star-arriba-fusion-calling
Public
A standardized snakemake workflow to map RNAseq reads with star and call fusions on the resulting alignment files with arriba.
Python
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MIT License
•0•0•0•1•Updated Feb 23, 2026Feb 23, 2026
microsatellite-instability-detection-with-msisensor-pro
Public
Best practices snakemake workflow for microsatellite instability (MSI) detection with msisensor-pro.
Python
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MIT License
•1•2•0•0•Updated Feb 10, 2026Feb 10, 2026
snakemake-workflow-template
Public template
A template for standard compliant snakemake-workflows
Python
•
MIT License
•43•125•2•0•Updated Jan 20, 2026Jan 20, 2026
rna-seq-star-deseq2
Public
RNA-seq workflow using STAR and DESeq2
snakemake deseq2 reproducibility
snakemake deseq2 reproducibility sciworkflows gene-expression-analysis
Python
•
MIT License
•210•352•2•0•Updated Dec 18, 2025Dec 18, 2025
effect-size-estimation
Public
Generic, uncertainty aware, parameter free effect size estimation
Python
•0•1•0•0•Updated Dec 1, 2025Dec 1, 2025
structure-based-screening
Public
Workflow for screening massive amounts of small molecules (ligands) against a target (PDB-File)
Python
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MIT License
•1•3•0•2•Updated Nov 17, 2025Nov 17, 2025
cellranger-count
Public
A Snakemake workflow for counting single cell RNAseq (scRNA-seq) data with Cell Ranger (Cell Ranger licensing requires a manual download of the software).
Python
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MIT License
•0•1•0•0•Updated Oct 14, 2025Oct 14, 2025
dna-seq-short-read-circle-map
Public
A snakemake workflow for calling extrachromosomal circular DNA in Illumina short-read sequencing data with Circle-Map
Python
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MIT License
•0•0•0•2•Updated Jun 16, 2025Jun 16, 2025
oncology
Public
A work in progress Snakemake workflow for cohort studies in oncology
0•2•0•0•Updated Dec 10, 2024Dec 10, 2024
cyrcular-calling
Public
A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.
Python
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MIT License
•2•4•9•2•Updated Nov 8, 2024Nov 8, 2024
ngs-test-data
Public
A workflow for creating small NGS test data sets, useful for continuous integration.
snakemake ngs snakemake-workflows
snakemake ngs snakemake-workflows
Python
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MIT License
•14•24•0•1•Updated Aug 15, 2024Aug 15, 2024
circular-dna-read-simulation
Public
snakemake workflow for long and short read simulation of circular DNA
Python
•1•0•0•0•Updated Jun 18, 2024Jun 18, 2024
dna-seq-neoantigen-prediction
Public
Snakemake workflow for neoantigen prediction
Python
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MIT License
•5•15•8•1•Updated Sep 7, 2023Sep 7, 2023
dna-seq-gatk-variant-calling
Public
This Snakemake pipeline implements the GATK best-practices workflow
snakemake gatk reproducibility
snakemake gatk reproducibility sciworkflows genomic-variant-calling
Python
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MIT License
•148•262•18•3•Updated Jun 8, 2023Jun 8, 2023
single-cell-drop-seq
Public template
A SingleCell RNASeq pre-processing pipeline built on snakemake
Python
•
Creative Commons Attribution Share Alike 4.0 International
•47•14•0•0•Updated Jan 11, 2023Jan 11, 2023
single-cell-rna-seq
Public template
A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
R
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MIT License
•46•108•1•1•Updated Nov 22, 2022Nov 22, 2022
chipseq
Public
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
Python
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MIT License
•20•26•0•1•Updated Feb 3, 2022Feb 3, 2022
cookiecutter-snakemake-workflow
Public
A cookiecutter template for Snakemake workflows
snakemake snakemake-workflows cookiecutter-template
snakemake snakemake-workflows cookiecutter-template
Python
•
MIT License
•36•60•0•1•Updated Feb 2, 2022Feb 2, 2022
docs
Public
Documentation of the Snakemake-Workflows project
snakemake snakemake-workflows
snakemake snakemake-workflows
MIT License
•25•156•4•0•Updated Feb 2, 2022Feb 2, 2022
species-quantification
Public
A Snakemake workflow for species quantification with kraken2+bracken.
Python
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MIT License
•0•2•0•0•Updated Sep 6, 2021Sep 6, 2021
cite-seq-alevin-fry-seurat
Public
Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat
R
•1•3•0•0•Updated May 27, 2021May 27, 2021
rad-seq-stacks
Public
Python
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MIT License
•1•1•8•0•Updated Jan 14, 2021Jan 14, 2021
accel-amplicon-trimming
Public template
Snakemake workflow implementing Accel Amplicon (Swift) trimming guidelines.
Python
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MIT License
•3•4•0•0•Updated May 18, 2019May 18, 2019