PhyloPi: An affordable, purpose built phylogenetic pipeline for the HIV drug resistance testing facility.

Phillip Armand BesterAndrie De VriesStephanus RiekertKim SteegenGert van ZylDominique Goedhals

Published in: PloS one (2019)

The Raspberry Pi image for PhyloPi, source code of the pipeline, sequence data, bash-, python- and R-scripts for the logistic regression, benchmarking as well as helper scripts are available at http://scholar.ufs.ac.za:8080/xmlui/handle/11660/7638 and https://github.com/ArmandBester/phylopi. The PhyloPi image and the source code are published under the GPLv3 license. A demo version of the PhyloPi pipeline is available at http://phylopi.hpc.ufs.ac.za/.

Keyphrases

deep learning
antiretroviral therapy
human immunodeficiency virus
hiv aids
dendritic cells
hiv testing
systematic review