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.

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

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.

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

Snakemake pipeline for simulating shotgun metagenomic samples

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

Long RNA-seq analysis workflow

Workflow for identifying and classifying homologous gene/protein sequences

Config files for my GitHub profile.

TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis

Lightweight bioinformatics pipeline for microbial genome recovery

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

Snakemake-based computational workflow for neoantigen prediction from diverse sources

Repo to analyze population genetic data with many different methods

Pipeline for automatic processing and quality control of mass spectrometry data

Simple template for running snakemake with R

NanoASV official repo

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

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

snakemake workflow for basecalling and demultiplexing of ONT sequencing data

Python pipeline for analyzing INSeq Insertion Sequencing data

A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.

Snakemake workflow for CRISPR-Cas9 screen analysis

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

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.

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.

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

:snake::hamburger: A beginner's guide to modular snakemake workflows.

hla-typing by optitype & polysolver , detect loh by lohhla.

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