Data

Tools

Indexes

Applications

Experiments

Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with snakemake-workflow

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

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/centrefornetzero/pypsa-fes

A model that optimises investment and operation, and incorporates flexibility domestic demand flexibility to model scenarios for Great Britain's future energy system.

demand-flexibility energy energy-model energy-system-model energy-transition great-britain modelling open-source optimization power-systems pypsa python sector-coupling snakemake-workflow

Last synced: 07 May 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/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/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/niekwit/crispr-screens

Snakemake workflow for CRISPR-Cas9 screen analysis

bioinformatics-pipeline crispr-screen-analysis snakemake-workflow

Last synced: 16 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/chazeon/dpgen-snakemake

A lightweight Snakemake-based workflow that implements the DP-GEN scheme.

ab-initio deep-learning machine-learning-potential snakemake-workflow workflow

Last synced: 10 Oct 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/niekwit/damid-seq

DamMapper: Snakemake workflow for DamID-Seq analysis

bioinformatics-pipeline damid snakemake-workflow

Last synced: 16 Jan 2026

https://github.com/niekwit/gps-orfeome

GPSW: A Snakemake workflow for GPS-ORFeome screens

bioinformatics protein-stability snakemake snakemake-workflow

Last synced: 16 Jan 2026

https://github.com/echosingh/echosingh

This repository serves as the foundation of my GitHub profile README, highlighting my projects, technical skills, and professional journey. It provides an overview of my contributions to open-source, personal projects, and areas of interest, while also reflecting my commitment to continuous learning and innovation.

github-action lowlighter-metrics metrics my-learning profile profile-card profile-readme readme readme-profile snakemake-workflow special-readme special-repository svg-images wakatime-stats

Last synced: 22 Jan 2026

https://github.com/open2c/distiller-sm

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

bioinformatics bioinformatics-pipeline hi-c hic snakemake snakemake-pipeline snakemake-workflow

Last synced: 16 Jul 2025

https://github.com/gustaveroussy/rna-count-kallisto

Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto

bioinformatics conda fastqc json-schema kallisto multiqc reproducible-workflows snakemake snakemake-workflow

Last synced: 11 Feb 2026

https://github.com/bcgsc/impala

Integrated Mapping and Profiling of Allelically-expressed Loci with Annotations

allele-specific-expression bioinformatics cancer snakemake-workflow

Last synced: 10 Aug 2025

https://github.com/moha-cm/autornaseq

Simplified RNA-Seq Insights with automation

conda flask-application mamba python r snakemake-pipeline snakemake-workflow

Last synced: 22 Jan 2026

https://github.com/akbaritabar/internal-and-international-migration-of-scientists

Scripts, data, and replication materials for "Global subnational estimates of migration of scientists reveal large disparities in internal and international flows"

internal-migration international-migration migration scholarly-migration scientific-mobility snakemake snakemake-workflow

Last synced: 19 May 2026

https://github.com/akbaritabar/course-session-on-other-computational-social-science-skills

Materials for course on ""Other" Computational Social Science Skills" at the fourth MPIDR Summer Incubator Program, June 10, 2025, Rostock, Germany (and online)

computational-social-science css-skills dask duckdb graph-databases parallel-computing snake-make snakemake-workflow

Last synced: 28 Aug 2025

https://github.com/tdayris/fair_gatk_mutect2

Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2

fair gatk-bestpractices mutect2 reproducible-workflows snakemake snakemake-workflow variant-calling

Last synced: 16 Jan 2026

https://github.com/mpusp/snakemake-simple-mapping

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

bowtie2 bwa-mem2 genomics mapping next-generation-sequencing snakemake snakemake-workflow star-alignment variant-calling

Last synced: 11 Mar 2026

https://github.com/thibaultlatrille/micmac

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

scientific-papers snakemake-workflow

Last synced: 08 Jan 2026

https://github.com/ctubbs750/snakemake-genome-bottle

Snakemake workflow to install reference genomes and their supporting files

gencode installer reference-genome snakemake-workflow

Last synced: 30 Apr 2025

https://github.com/thibaultlatrille/selcoeff

Estimating the proportion of beneficial mutations that are not adaptive in mammals

scientific-papers snakemake-workflow

Last synced: 15 Feb 2026

https://github.com/datasnakes/orthoevol-snakemake

A snakemake workflow for the OrthoEvol python package.

orthoevol orthology-inference snakemake snakemake-pipelines snakemake-workflow

Last synced: 06 Jun 2026

https://github.com/kzkedzierska/atac

ATAC-seq snakemake pipeline

atac-seq snakemake snakemake-workflow

Last synced: 26 Apr 2026

https://github.com/meeranhussain/population_genomic_analysis

A repository for efficient population genomic analysis using Snakemake workflow.

genome-analysis ngs ngs-analysis population population-genomics rprogramming snakemake-workflow variant-calling whole

Last synced: 25 Feb 2025

https://github.com/massiddamt/rna_vc_docker

A Snakemake pipeline for RNA Seq Variant Calling

pipeline rnaseq snakemake-workflow

Last synced: 29 Mar 2025

https://github.com/meeranhussain/rnaseq_deseq2_snakemake

Differential gene expression analysis for samples with replicates using STAR-DeSeq2 pipeline

deseq2-analysis differential-gene-expression rna rna-seq-analysis rna-seq-pipeline snakemake-workflow star-aligner

Last synced: 12 Jun 2026

https://github.com/person-c/bulkrnaseq_snakemake

Snakemake workflow for bulkRNAseq

rna-seq snakemake-workflow

Last synced: 20 Jan 2026

https://github.com/ccbr/ccbr_circrna_ampliconseq

Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.

amplicon-pipeline amplicon-sequencing circrna circrna-pipeline snakemake-workflow

Last synced: 29 Jan 2026

https://github.com/tdayris/fair_macs2_calling

Snakemake workflow used to call peaks with Macs2

bowtie2 homer macs2 sambamba snakemake snakemake-workflow snakemake-wrappers

Last synced: 16 Jan 2026

https://github.com/tdayris/fair_bowtie2_mapping

Align reads over a reference genome, filter aligned-reads, and mark duplicates

bowtie2 multiqc sambamba snakemake snakemake-workflow snakemake-wrappers

Last synced: 16 Jan 2026

https://github.com/tdayris/fair_genome_indexer

Download and index Ensembl sequences and annotations, remove non-canonical chromosimes, remove low TSL, index with multiple tools

ensembl fair snakemake snakemake-workflow snakemake-wrappers

Last synced: 16 Jan 2026

https://github.com/pooranibcbb/virome-pipeline

This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diversity in metagenomes.

bioinformatics-pipeline snakemake-workflow viral-metagenomics

Last synced: 26 Jul 2025

https://github.com/lumc/gnomad-merge

Snakemake pipeline to merge gnomAD VCF files

ngs ngs-analysis snakemake snakemake-workflow

Last synced: 24 Mar 2025

https://github.com/meeranhussain/rnaseq_degseq_snakemake_no-replicates

Workflow for differential gene expression analysis for non-replicate samples using DEGseq

differential-gene-expression rna-seq-analysis rna-seq-pipeline snakemake-workflow star-aligner

Last synced: 13 Jun 2026

https://github.com/liao961120/minimal-snake

An enhanced template structure for Snakemake

git-bash make python reproducibility snakemake snakemake-workflow windows

Last synced: 28 Apr 2026