snakemake-pipeline

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

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

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.

NeoGuider, neoepitope detection using advanced feature engineering

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.

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.

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

Reference-guided reanalysis of published finger millet (Eleusine coracana) drought RNA-seq against the chromosome-scale KNE 796-S assembly, with a documented audit of four analytical defects found and corrected.