Longitudinal analysis of high-risk HPV infections reveals within-host viral genome changes over time

This repository contains patient phenotype data, HPV genomic variant data, HPV consensus sequences, and sequenced HPV reads aligned to high-risk HPV reference genomes generated as part of the study “Longitudinal analysis of high-risk HPV infections reveals within-host viral genome changes over time”. The high-risk HPV reference genomes and the pipeline used to process the sequencing data can be found at https://github.com/NCI-CGR/HPV_Guanacaste_CostaRica_Longitudinal_Study. To facilitate upload and download of the large sequencing dataset, the BAM files deposited in this repository were packaged into compressed archive files, which were subsequently split into multiple parts. After downloading all parts from this repository, users should first concatenate the split files to reconstruct the original compressed archives using the following commands: cat bam_files_set1_part_* > bam_files_set1.tar.gz cat bam_files_set2_part_* > bam_files_set2.tar.gz Once the original compressed archives have been reconstructed, the individual BAM files can be extracted using: tar -zxvf bam_files_set1.tar.gz The same command can be used to extract files from bam_files_set2.tar.gz.