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.
Project for apaQTL MS. The workflowr project apaQTL by brimittleman
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
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
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.
Fine mapping analysis within the pQTL pipeline project
barthez-kenwou is a ✨special ✨ repository that I used to add a README.md to my GitHub profile. I discorved it when i studied how to write and add a good and beautiful readme file to my projet 🥲✌️
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
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