A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.

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.

A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.

reproducible research project template for R using Renv and snakemake with an econ application

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

Workflow for identifying and classifying homologous gene/protein sequences

Snakemake pipeline for simulating shotgun metagenomic samples

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Config files for my GitHub profile.

Repo to analyze population genetic data with many different methods

Long RNA-seq analysis workflow

Snakemake-based computational workflow for neoantigen prediction from diverse sources

Simple template for running snakemake with R

Lightweight bioinformatics pipeline for microbial genome recovery

This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis

🐍🍔 A beginner's guide to modular snakemake workflows.

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

snakemake workflow for basecalling and demultiplexing of ONT sequencing data

Python pipeline for analyzing INSeq Insertion Sequencing data

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