snakemake workflows developed for Coriell Bioinformatics

Current Workflows:

• Paired-end RNA-seq processing and quantification
• PAired-end ATAC-seq processing and peak calling with Genrich
• De novo transcript assembly and quantification
• Somatic variant calling from tumor-normal WES/WGS data
• Estimation of bacterial read abundance from sequencing data using Kraken2 and Braken

Caveats

All of the workflows assume you're working on Coriell's bioinformatics servers which means software environments and paths to pre-generated genome indeces and system resources will not work on your machine.