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Projects in Awesome Lists tagged with snakemake

A curated list of projects in awesome lists tagged with snakemake .

https://github.com/snakemake/snakemake

This is the development home of the workflow management system Snakemake. For general information, see

reproducibility snakemake workflow-management

Last synced: 29 Jan 2026

https://github.com/crazyhottommy/rna-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Last synced: 16 May 2025

https://github.com/crazyhottommy/RNA-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Last synced: 06 May 2025

https://github.com/PyPSA/pypsa-eur

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

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

Last synced: 07 May 2025

https://github.com/pypsa/pypsa-eur

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

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

Last synced: 19 Feb 2026

https://github.com/maxplanck-ie/snakepipes

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

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

Last synced: 17 Mar 2026

https://github.com/metagenome-atlas/atlas

ATLAS - Three commands to start analyzing your metagenome data

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

Last synced: 15 May 2025

https://github.com/franciscozorrilla/metagem

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

Last synced: 25 Jun 2025

https://github.com/snakemake/snakefmt

The uncompromising Snakemake code formatter

bioinformatics black code codeformatter fmt formatter python snakemake

Last synced: 09 Feb 2026

https://github.com/franciscozorrilla/metaGEM

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

Last synced: 11 Apr 2025

https://github.com/vanheeringen-lab/seq2science

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.

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

Last synced: 21 Aug 2025

https://github.com/jdblischak/smk-simple-slurm

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

bioinformatics slurm snakemake snakemake-profile

Last synced: 06 May 2025

https://github.com/sequana/sequana

Sequana: a set of Snakemake NGS pipelines

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

Last synced: 17 Jan 2026

https://github.com/crazyhottommy/pyflow-chipseq

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

chip-seq python snakemake

Last synced: 06 May 2025

https://github.com/epigen/atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

atac-seq bash bioinformatics biomedical-data-science ngs pipeline python snakemake workflow

Last synced: 07 Mar 2026

https://github.com/slowkow/snakefiles

:snake: Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).

bioinformatics high-performance-computing lsf-jobs python rna-seq snakemake

Last synced: 14 Apr 2025

https://github.com/snakemake-workflows/dna-seq-varlociraptor

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.

genomic-variant-calling reproducibility sciworkflows snakemake varlociraptor

Last synced: 25 May 2026

https://github.com/crazyhottommy/pyflow-ATACseq

ATAC-seq snakemake pipeline

atac-seq snakemake

Last synced: 10 May 2025

https://github.com/crazyhottommy/pyflow-atacseq

ATAC-seq snakemake pipeline

atac-seq snakemake

Last synced: 06 May 2025

https://github.com/4dn-dcic/tibanna

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.

aws aws-lambda aws-step-function bioinformatics conda cwl cwl-workflow docker ot2od032119 pipelines snakemake snakemake-workflow u01ca200059 wdl wdl-workflow

Last synced: 18 Jan 2026

https://github.com/jetbrains-research/snakecharm

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

bioinformatics-pipeline bioinformatics-tool intellij intellij-plugins pycharm python snakemake

Last synced: 09 Apr 2025

https://github.com/cihga39871/pipelines.jl

A lightweight and powerful Julia package for computational pipelines and workflows.

bioinformatics bioinformatics-pipeline computational-pipelines julia pipeline pipelines ruffus snakemake workflow workflows

Last synced: 21 Aug 2025

https://github.com/shandley/hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

snakemake viral-metagenomes virome

Last synced: 23 Mar 2025

https://github.com/epigen/enrichment_analysis

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

atac-seq bioinformatics biomedical-data-science chip-seq enrichment-analysis gene-set-enrichment gene-sets genomic-regions motif-enrichment-analysis pipeline rna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/timtroendle/cookiecutter-reproducible-research

A cookiecutter template for reproducible research projects using Python, Snakemake, and Pandoc.

automation cluster-computing cookiecutter-template pandoc python reproducible-research snakemake

Last synced: 30 Dec 2025

https://github.com/kyleam/snakemake-mode

[MIRROR] Emacs support for Snakemake

emacs-lisp snakemake

Last synced: 11 Apr 2025

https://github.com/PyPSA/247-cfe

Explore the impacts of 24/7 Carbon-Free Energy PPAs

energy energy-model power-system pypsa snakemake

Last synced: 07 May 2025

https://github.com/pypsa/247-cfe

Explore the impacts of 24/7 Carbon-Free Energy PPAs

energy energy-model power-system pypsa snakemake

Last synced: 15 Apr 2025

https://github.com/saketkc/rna-seq-snakemake

Snakemake based pipeline for RNA-Seq analysis

bioinformatics pipeline rna-seq-analysis rna-seq-snakemake snakemake

Last synced: 22 Oct 2025

https://github.com/epigen/dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow

Last synced: 15 Apr 2025

https://github.com/gagneurlab/fraser-analysis

Accompanying analysis code for the FRASER manuscript

outlier-detection r rare-disease rna-seq snakemake workflow

Last synced: 11 Apr 2025

https://github.com/epigen/unsupervised_analysis

A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.

cluster-analysis cluster-validation clustering clustering-algorithm clustree data-science data-visualization densmap dimensionality-reduction heatmap high-dimensional-data leiden-algorithm pca principal-component-analysis snakemake umap unsupervised-learning visualization workflow

Last synced: 15 Apr 2025

https://github.com/crazyhottommy/pyflow-rnaseq

RNAseq pipeline based on snakemake

rnaseq snakemake

Last synced: 06 May 2025

https://github.com/daylily-informatics/daylily

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

aws bioinformatics bioinformatics-pipeline budgeting cwl ec2 ephemeral genomic-data-analysis giab human-genome informatics ngs parallel-cluster scalable scaling slurm snakemake snv-call wgs

Last synced: 19 Jun 2025

https://github.com/aryarm/varca

Use an ensemble of variant callers to call variants from ATAC-seq data

atac-seq-data machine-learning random-forest snakemake variant-calling

Last synced: 11 Apr 2025

https://github.com/mcvickerlab/varca

Use an ensemble of variant callers to call variants from ATAC-seq data

atac-seq-data machine-learning random-forest snakemake variant-calling

Last synced: 01 Apr 2026

https://github.com/epigen/scrnaseq_processing_seurat

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

10xgenomics bioinformatics biomedical-data-science cite-seq sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/genome_tracks

A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.

atac-seq bioinformatics biomedical-data-science genome-browser genome-track genomic-regions pipeline python rna-seq scrna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/open2c/quaich

snakemake pipeline for Hi-C post-processing

analysis hi-c snakemake workflow

Last synced: 24 Apr 2025

https://github.com/epigen/dea_seurat

A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization volcano-plot workflow

Last synced: 14 Jun 2025

https://github.com/tjbencomo/ngs-pipeline

Pipeline for Somatic Variant Calling with WES and WGS data

bioinformatics exome-sequencing snakemake somatic-variants

Last synced: 04 Mar 2026

https://github.com/epigen/mixscape_seurat

A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.

bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow

Last synced: 22 Aug 2025

https://github.com/epigen/spilterlize_integrate

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

atac-seq batch-effect bioinformatics biomedical-data-science chip-seq confounding-effects count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow

Last synced: 24 Aug 2025

https://github.com/krassowski/nbpipeline

Snakemake-like pipeline manager for reproducible Jupyter Notebooks

jupyter jupyter-notebook snakemake

Last synced: 13 Apr 2025

https://github.com/nh13/snakesee

A terminal UI for monitoring Snakemake workflows

bioinformatics monitor python snakemake terminal tui workflow

Last synced: 02 Apr 2026

https://github.com/sci-f/snakemake.scif

Tutorial with snakemake and Scientific Filesystem

scientific-filesystem scif snakemake

Last synced: 30 Mar 2025

https://github.com/epigen/cemm.slurm.sm

CeMM's Snakemake SLURM cluster profile

cluster-profile slurm snakemake

Last synced: 15 Apr 2025

https://github.com/helenalc/simulation-comparison

Snakemake workflow to benchmark scRNA-seq data simulators

benchmark scrna-seq simulation snakemake

Last synced: 21 Sep 2025

https://github.com/saketkc/riboraptor

Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)

bioinformatics bioinformatics-pipeline genomics riboseq ribosome-profiling snakemake

Last synced: 12 Jun 2025

https://github.com/biocore/qadabra

Snakemake workflow for comparison of differential abundance ranks

bioinformatics differential-abundance machine-learning metagenomics microbiome pipeline snakemake workflow

Last synced: 13 May 2025

https://github.com/pdimens/lepwrap

A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.

bioinformatics genome-assembly linkage linkage-mapping snakemake

Last synced: 20 Sep 2025

https://github.com/jakelever/biotext

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

bioc pubmed pubmed-central pubtator snakemake text-mining

Last synced: 16 Jan 2026

https://github.com/adonath/snakemake-workflow-fermi-lat

A Snakemake workflow for Fermi-LAT data reduction

data-reduction fermi-lat fermitools gammapy snakemake

Last synced: 17 Nov 2025

https://github.com/nbisweden/nbis-meta

A snakemake workflow for metagenomic projects

assembly metagenomics snakemake workflow

Last synced: 05 Mar 2025

https://github.com/schlosslab/mikropml-snakemake-workflow

Snakemake template for building reusable and scalable machine learning pipelines with mikropml

machine-learning rstats snakemake

Last synced: 30 Oct 2025

https://github.com/RickGelhausen/HRIBO

We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional characterization.

bioinformatics prokaryotes ribosome-profiling snakemake

Last synced: 10 Jul 2025

https://github.com/fritzbayer/snakemake-with-r

Simple template for running snakemake with R

r-workflow snakemake snakemake-pipeline snakemake-workflow

Last synced: 27 Sep 2025

https://github.com/irieo/space-time-optimization

Code for the paper "Spatio-temporal load shifting for truly clean computing"

energy power-systems pypsa snakemake

Last synced: 15 Oct 2025

https://github.com/jfallmann/monsda

MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

hts nextflow ngs pipeline snakemake

Last synced: 02 Apr 2025

https://github.com/smutch/snakedoc

A Sphinx extension for Snakemake workflows

snakemake sphinx-extension

Last synced: 25 Jan 2026

https://github.com/aryarm/as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq

allele-specific-expression atac-seq rna-seq snakemake whole-genome-sequencing

Last synced: 11 Apr 2025

https://github.com/cbrueffer/snakemake-aws-parallelcluster-slurm

Snakemake profile for running on AWS ParallelCluster with the Slurm scheduler

aws aws-parallelcluster parallelcluster profile snakemake

Last synced: 11 Apr 2025

https://github.com/cbg-ethz/pybda

:computer::computer::computer: A commandline tool for analysis of big biological data sets for distributed HPC clusters.

apache-spark big-data machine-learning python snakemake

Last synced: 24 Jul 2025

https://github.com/thibaultlatrille/salmonscholar

Don't get drowned in the flood of scientific publications. As a salmon, climb up to the stream.

bibliography scholarly-articles snakemake

Last synced: 22 Apr 2025

https://github.com/fischuu/snakebite-holoruminant-metag

Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators

dna metagenome-assembled-genomes metagenomics snakemake snakemake-workflow

Last synced: 18 Feb 2026

https://github.com/openomics/snakevision

An awesome tool to visualize snakemake rule graphs

dag dagviz dot-graphics networkx rulegraph snakemake visualization

Last synced: 02 May 2026

https://github.com/semenko/serpent-methylation-pipeline

An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq samples, including cfDNA.

bisulfite bs-seq bsseq em-seq emseq epigenetics methylation pipeline snakemake

Last synced: 26 Jan 2026

https://github.com/mpusp/snakemake-crispr-guides

A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.

bioinformatics-pipeline crispr crispr-design guide-rna-library python3 r-markdown snakemake snakemake-workflow workflow

Last synced: 27 Apr 2026

https://github.com/jhrcook/pymc3-stan-comparison

Comparing the performance of the probabilistic programming languages PyMC3 and Stan.

probabilistic-programming pymc3 snakemake stan

Last synced: 28 Oct 2025

https://github.com/jackhump/wgs-qc-pipeline

A Snakemake pipeline for Quality Control of Whole Genome Sequencing data

snakemake wgs

Last synced: 18 Jan 2026

https://github.com/truwl/capanno

cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.

cwl nextflow snakemake wdl

Last synced: 10 Mar 2025

https://github.com/snakemake/snakemake-tutorial-data

Example data for the official Snakemake tutorial

reproducibility snakemake tutorial

Last synced: 23 Feb 2025

https://github.com/jma1991/chromium

A Snakemake workflow to process scRNA-seq data from 10x Genomics

snakemake

Last synced: 17 Jan 2026

https://github.com/dohlee/snakemake-hamburger

:snake::hamburger: A beginner's guide to modular snakemake workflows.

bioinformatics-pipeline reproducible-research snakemake snakemake-workflow

Last synced: 29 Apr 2025

https://github.com/mbhall88/head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.

bioinformatics clustering diagnostics drug-resistance illumina nanopore pipeline snakemake transmission tuberculosis

Last synced: 09 Jul 2025

https://github.com/snakemake/snakemake-tutorials

start of repository with various snakemake tutorials (under development)

google-cloud snakemake snakemake-tutorials tutorials under-development

Last synced: 27 Feb 2026

https://github.com/zavolanlab/mirflowz

Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.

bioinformatics isomirs mirna snakemake workflow

Last synced: 16 Jan 2026

https://github.com/solida-core/solida

SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.

ansible ngs ngs-pipeline pipeline python reproducibility snakemake workflow yaml

Last synced: 23 Apr 2025

https://github.com/metagenlab/diag_pipelines

Pipelines dealing with high throughput sequencing data for microbiology diagnostic procedures. Documentation available at http://metagenlabdiag-pipelines.readthedocs.io/en/latest/ and Docker images at https://hub.docker.com/r/metagenlab/diag_pipelines/.

bioinformatics conda-environment genomics microbiology snakemake

Last synced: 19 Feb 2026

https://github.com/dohlee/snakemake-bismark-methyldackel

Bismark-MethylDackel DNA methylation quantification pipeline in snakemake.

bioinformatics methylation pipeline reproducible-research reproducible-science snakemake snakemake-pipelines

Last synced: 05 May 2025

https://github.com/niekwit/rna-seq-salmon-deseq2

Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2

bioinformatics snakemake snakemake-workflow

Last synced: 16 Jan 2026

https://github.com/jjjermiah/snakemake-pixi-template

A basic template to get started with Snakemake using Pixi

pixi snakemake

Last synced: 02 Jul 2025

https://github.com/gibsramen/xebec

Snakemake pipeline for microbiome diversity effect size benchmarking

bioinformatics microbiome pipeline snakemake

Last synced: 13 May 2025

https://github.com/sebastian-gregoricchio/snhic

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

compartments dchic genova hi-c hic hicexplorer loop selfish snakemake snakemake-pipeline stripenn tad

Last synced: 31 May 2026

https://github.com/supermaxiste/arpeggio

A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.

allopolyploid automation bisulfite-sequencing dna-methylation epigenetics plants reproducibility snakemake whole-genome-sequencing workflow

Last synced: 04 Mar 2026

https://github.com/openomics/nanite

A streamlined Oxford Nanopore Viral Metagenomics Pipeline

annotation assembly classification pathogen-surveillance pipeline singularity slim snakemake viral-metagenomics

Last synced: 18 Jan 2026

https://github.com/bioconda/bioconda-paper

Data analysis related to the bioconda paper

analysis-workflows bioconda reproducibility snakemake

Last synced: 23 Apr 2025