ERV identification, annotation and quantification pipeline built for ccbr1271. This pipeline detects and quantifies Endogenous Retroviruses using the scripts obtained from the Belkaid group.
- This pipeline built using Snakemake.
- This pipeline uses modules preinstalled and available on BIOWULF.
- This pipeline takes adapter removed and preprocess FASTQs from ccbr1271_longRNA pipeline as inputs.
- This pipeline has 3 distinct branches:
- Alignment with STAR followed by repeat elements quantification using HOMER
- Assembly of reads using MEGAHIT followed by contig alignments with NR database using DIAMOND
- Quantification + annotation of human ERVs using the hervQuant pipeline