A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards

Simple template for running snakemake with R

A comprehensive quality-control and quantification RNA-seq pipeline

A Snakemake workflow to filter, annotate and prepare variant call format (VCF) data for scout using GATK4, SnpSift, VEP and genmod. Designed to be used after human_genomics_pipeline.

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

Project for apaQTL MS. The workflowr project apaQTL by brimittleman

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

NeoGuider, neoepitope detection using advanced feature engineering

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.

population structural variant calling with smoove

Fine mapping analysis within the pQTL pipeline project

CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous computing environments.

Short read mapping and variant calling

Pipeline for analyses of multiple pathogens, like SARS-CoV-2 with positivity rate analyses

This repo contains scripts and workflows for performing bulk transcriptomics analyses

A small snakemake pipeline to perform quality analysis of RNA-Seq data with FastQC.