HPV-genotyping

--David B. Stern, Ph.D.--

The pipeline was developed to process Illumina sequencing data generated from CD Genomic's HPV Capture Kit.

Usage

The scripts directory contains bash and R scripts to process the data.

The ref directory contains a fasta file of papillomavirus reference genomes from PaVE, including non-reference genomes, borrowed from HPV-EM which has nicely reformatted names. This reference fasta needs to be indexed by Bowtie 2

All scripts rely on a file called files.txt which contains the names of all the samples to be processed.

• clean_map_abundance.sh: UGE array script to clean reads with bbduk, map reads to the reference genomes with Bowtie 2, and estimate the relative abundance of each genotype using msamtools.

• stats.sh: Collects coverage and pairwise ID statistics from the bam files using awk and NanoStat, and generates coverage plots using collect_stats.R. Should be run from the directory with the bam files. Be sure to check paths for reference fasta, index, and collect_stats.R

• collect_stats.R: R script to generate table of statistics and coverage plots. Run automatically with stats.sh. Requires the tidyverse R package.

• merge_msamtools_stats.R: R script to merge the output of msamtools and collect_stats.R for each sample.