`prepdrm`

Analysis pipeline for identifying low frequency drug resistance mutations (DRMs) in samples from the Partners PrEP study.

Manuscript in preparation.

Running

The provisioning/ directory contains Ansible scripts for installing all required dependencies and data - look there for details.

Alternatively, use one of these options:

On AWS: the AMI ami-0ccca73c in us-west-2 has all necessary dependencies and control data pre-loaded. Login as ubuntu.
Using Vagrant: run vagrant up.
Using the Docker image cmccoy/prepdrm: docker pull cmccoy/prepdrm; docker run -i -t -P cmccoy/prepdrm /bin/bash.

Data

Data from control samples in FASTQ format are available at https://s3-us-west-2.amazonaws.com/prepdrm454controls/prepdrm454controls.tar.

License

GPL v3 - see COPYING