The scripts contained in this repository were used in part to produce some or all of the results found in "Deep sequencing of protease inhibitor resistance HIV patient isolates reveals patterns of correlated mutations in gag and protease".

Most of these scripts were written between 2013-2014, and the manuscript preparation and review took most of 2014, so these scripts are a bit outdated.

Also note that there is (a) no guarantee that the output of these scripts ended up in the manuscript or (b) these are the correct/final versions of the scripts because there are several unversioned copies flying around in different places and I snagged these versions from a backup made around 2014/04/04. That said, I will attempt to clean them up over time, but wanted to commit (what may be) the originals so there is a public review history. The majority of the scripts need:

• File paths cleaned up
• Commented-out/unused/broken methods revised or removed
• Directory structure fixed as they did not previously exist in a single directory

The raw sequencing data (fastq), aligned and cleaned files (bam/sam), and SNP/amino acid substitution databases are excluded from this repository due to the private nature of patient information. Additional information regarding IRB documentation or data sources can be found in published manuscript. The scripts herein have been cleaned of any analysis methods that invoke specific patient identifiers (anonymized IDs and sample numbers) so that nothing is revealed.