Snakemake-Workflows

All

26 repositories

rna-seq-kallisto-sleuth
Public
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
rna-seq snakemake reproducibility differential-expression sciworkflows kallisto sleuth
Python
•
MIT License
•45•68•7•2•Updated Jul 16, 2025Jul 16, 2025
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•12•7•4•Updated Jul 15, 2025Jul 15, 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•0•0•0•Updated Jul 11, 2025Jul 11, 2025
rna-longseq-de-isoform
Public
long read differential expression analysis and splice variant analysis
gene-annotation differential-expression isoform-quantification
Python
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MIT License
•1•3•8•2•Updated Jul 4, 2025Jul 4, 2025
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) via the unified statistical model of Varlociraptor.
snakemake reproducibility sciworkflows genomic-variant-calling varlociraptor
Python
•
MIT License
•42•86•8•14•Updated Jul 4, 2025Jul 4, 2025
snakemake-workflow-template
Public template
A template for standard compliant snakemake-workflows
Python
•
MIT License
•38•105•1•1•Updated Jun 23, 2025Jun 23, 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
effect-size-estimation
Public
Generic, uncertainty aware, parameter free effect size estimation
Python
•0•0•0•0•Updated May 15, 2025May 15, 2025
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•1•Updated Mar 26, 2025Mar 26, 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•3•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
Python
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MIT License
•14•22•0•1•Updated Aug 15, 2024Aug 15, 2024
rna-seq-star-deseq2
Public
RNA-seq workflow using STAR and DESeq2
reproducibility sciworkflows gene-expression-analysis snakemake deseq2
Python
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MIT License
•209•343•1•5•Updated Aug 1, 2024Aug 1, 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•14•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 sciworkflows genomic-variant-calling
Python
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MIT License
•145•255•18•3•Updated Jun 8, 2023Jun 8, 2023
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•2•0•0•Updated Feb 9, 2023Feb 9, 2023
single-cell-drop-seq
Public template
A SingleCell RNASeq pre-processing pipeline built on snakemake
Python
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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
•45•102•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
Python
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MIT License
•37•59•0•1•Updated Feb 2, 2022Feb 2, 2022
docs
Public
Documentation of the Snakemake-Workflows project
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•2•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