A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
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Updated
Jan 13, 2023 - Python
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
A comprehensive quality-control and quantification RNA-seq pipeline
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
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.
Simple template for running snakemake with R
Project for apaQTL MS. The workflowr project apaQTL by brimittleman
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards
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.
A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.
population structural variant calling with smoove
A small snakemake pipeline to perform quality analysis of RNA-Seq data with FastQC.
This repo contains scripts and workflows for performing bulk transcriptomics analyses
Short read mapping and variant calling
A repository for RNA-seq workflow
🪆🦖 A snakemake wrapper around Nesvilab's FragPipe-CLI. In a perfect world, this pipeline was based on Sage.
Template directory for creating a snakemake pipeline
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