A template for standard compliant snakemake-workflows
☆125Jan 20, 2026Updated 2 months ago
Alternatives and similar repositories for snakemake-workflow-template
Users that are interested in snakemake-workflow-template are comparing it to the libraries listed below
Sorting:
- A workflow for creating small NGS test data sets, useful for continuous integration.☆24Aug 15, 2024Updated last year
- RNA-seq workflow using STAR and DESeq2☆352Dec 18, 2025Updated 3 months ago
- Cookiecutter for snakemake slurm profile☆134Apr 25, 2024Updated last year
- A statically generated catalog of available Snakemake workflows☆37Updated this week
- A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.☆68Feb 25, 2026Updated 3 weeks ago
- This is the development home of the Snakemake wrapper repository, see☆240Updated this week
- deploy a snakemake pipeline directly from version control (under development)☆25Mar 12, 2026Updated last week
- A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets☆13Mar 12, 2026Updated last week
- A cookiecutter template for Snakemake workflows☆60Feb 2, 2022Updated 4 years ago
- A Github action for running a Snakemake workflow☆62Dec 15, 2025Updated 3 months ago
- This Snakemake pipeline implements the GATK best-practices workflow☆262Jun 8, 2023Updated 2 years ago
- Documentation of the Snakemake-Workflows project☆156Feb 2, 2022Updated 4 years ago
- The uncompromising Snakemake code formatter☆183Updated this week
- A *fast* tool for BAM/CRAM quality evaluation, intended for long reads☆176Mar 2, 2026Updated 3 weeks ago
- This is the development home of the workflow management system Snakemake. For general information, see☆2,727Updated this week
- Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu☆16Mar 9, 2026Updated 2 weeks ago
- Snakemake tutorial materials☆19Mar 9, 2020Updated 6 years ago
- Snakemake workflow management system and CLI generation tool☆65Oct 22, 2025Updated 5 months ago
- Lightweight Python interfaces for reading, writing, and querying genomic regions (BED)☆14Nov 25, 2025Updated 3 months ago
- ⛰ covtobed | Convert the coverage track from a BAM file into a BED file☆44Nov 6, 2025Updated 4 months ago
- Language support and snippets for Snakemake workflows (Snakefile, *.smk) for Visual Studio Code and Apache Theia.☆23Mar 11, 2026Updated last week
- A Snakemake executor plugin for submitting jobs to a SLURM cluster☆48Mar 13, 2026Updated last week
- A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …☆89Updated this week
- A place to put docker build files☆13Oct 3, 2023Updated 2 years ago
- Genome scale metabolic models in SBML format☆10Nov 16, 2021Updated 4 years ago
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated last year
- A TUI for monitoring Snakemake workflows in real-time.☆54Mar 13, 2026Updated last week
- HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps☆14May 4, 2023Updated 2 years ago
- Best practices and workflow for genome annotation☆79Apr 14, 2025Updated 11 months ago
- Code associated with MIX-seq manuscript☆15Aug 26, 2020Updated 5 years ago
- A program for the analysis of single cell nanopore long read data☆20Jul 1, 2025Updated 8 months ago
- Analysis tool for NG-Capture-C, Tri-C and Tiled-C data☆10Oct 13, 2025Updated 5 months ago
- Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.☆22Feb 9, 2026Updated last month
- Documentation of the Snakemake-Profiles project.☆55Mar 15, 2022Updated 4 years ago
- Snakemake profile for running jobs on an LSF cluster☆38Jul 29, 2024Updated last year
- Arima Capture HiC pipeline (Arima-CHiC)☆12May 16, 2024Updated last year
- Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff☆52Oct 17, 2023Updated 2 years ago
- ☆16Mar 2, 2026Updated 3 weeks ago
- Listing of GPU based bioinformatics software & sites & publications☆12Jan 16, 2022Updated 4 years ago