A template for standard compliant snakemake-workflows
☆138Mar 27, 2026Updated 6 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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A workflow for creating small NGS test data sets, useful for continuous integration.☆23Aug 15, 2024Updated 2 years ago
- RNA-seq workflow using STAR and DESeq2☆371Oct 5, 2026Updated last week
- Cookiecutter for snakemake slurm profile☆136Apr 25, 2024Updated 2 years ago
- A statically generated catalog of available Snakemake workflows☆36Oct 5, 2026Updated last week
- A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.☆69Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- This is the development home of the Snakemake wrapper repository, see☆254Updated this week
- deploy a snakemake pipeline directly from version control (under development)☆28Sep 28, 2026Updated 2 weeks ago
- A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets☆13Oct 1, 2026Updated last week
- A cookiecutter template for Snakemake workflows☆59Feb 2, 2022Updated 4 years ago
- A Github action for running a Snakemake workflow☆63Apr 24, 2026Updated 5 months ago
- This Snakemake pipeline implements the GATK best-practices workflow☆267Jun 8, 2023Updated 3 years ago
- Documentation of the Snakemake-Workflows project☆160Feb 2, 2022Updated 4 years ago
- The uncompromising Snakemake code formatter☆196Sep 9, 2026Updated last month
- A *fast* tool for BAM/CRAM quality evaluation, intended for long reads☆190Oct 1, 2026Updated last week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Snakemake tutorial materials☆19Mar 9, 2020Updated 6 years ago
- An awesome tool to visualize snakemake rule graphs☆45May 2, 2026Updated 5 months ago
- This is the development home of the workflow management system Snakemake. For general information, see☆2,884Updated this week
- A TUI for monitoring Snakemake workflows in real-time.☆71Updated this week
- Language support and snippets for Snakemake workflows (Snakefile, *.smk) for Visual Studio Code and Apache Theia.☆25May 21, 2026Updated 4 months ago
- ⛰ covtobed | Convert the coverage track from a BAM file into a BED file☆44Nov 6, 2025Updated 11 months ago
- Lightweight Python interfaces for reading, writing, and querying genomic regions (BED)☆16Jul 10, 2026Updated 3 months ago
- Snakemake workflow management system and CLI generation tool☆67Oct 22, 2025Updated 11 months ago
- A Snakemake executor plugin for submitting jobs to a SLURM cluster☆56Sep 28, 2026Updated 2 weeks ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A place to put docker build files☆14Sep 11, 2026Updated last month
- Genome scale metabolic models in SBML format☆11Nov 16, 2021Updated 4 years ago
- A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …☆90Oct 6, 2026Updated last week
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated 2 years ago
- Arima Capture HiC pipeline (Arima-CHiC)☆14May 16, 2024Updated 2 years ago
- HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps☆14May 4, 2023Updated 3 years ago
- Best practices and workflow for genome annotation☆80Apr 14, 2025Updated last year
- Analyzes whole genome sequencing data for gene-editing verification☆13Aug 31, 2026Updated last month
- Code associated with MIX-seq manuscript☆15Aug 26, 2020Updated 6 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- A program for the analysis of single cell nanopore long read data☆22Jul 1, 2025Updated last year
- Snakemake profile for running jobs on an LSF cluster☆38Jul 29, 2024Updated 2 years ago
- Documentation of the Snakemake-Profiles project.☆55Mar 15, 2022Updated 4 years ago
- Analysis tool for NG-Capture-C, Tri-C and Tiled-C data☆10Jun 10, 2026Updated 4 months ago
- Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff☆51Oct 17, 2023Updated 2 years ago
- Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.☆22Feb 9, 2026Updated 8 months ago
- Listing of GPU based bioinformatics software & sites & publications☆12Jan 16, 2022Updated 4 years ago