A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

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.

Scalable open-source software to run, develop, and benchmark causal discovery algorithms

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

Snakemake pipeline for simulating shotgun metagenomic samples

Workflow for identifying and classifying homologous gene/protein sequences

Long RNA-seq analysis workflow

Snakemake-based computational workflow for neoantigen prediction from diverse sources

Lightweight bioinformatics pipeline for microbial genome recovery

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 CRISPR-Cas9 screen analysis

snakemake workflow for basecalling and demultiplexing of ONT sequencing data

Python pipeline for analyzing INSeq Insertion Sequencing data

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

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

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

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

Snakemake workflows for TAM depletion analysis and de novo IS605 annotation

The pipeline to process Novaseq dataset, from fastq to nge.