A high-throughput multiplexed amplicon sequencing workflow to quantify drug resistance mutations (DRMs) against protease, reverse transcriptase and integrase inhibitors

The detection of drug resistance mutations (DRM) in minor viral populations is of potential clinical importance. However, sophisticated computational infrastructure and competence for analysis of high throughput sequence (HTS) data is lacking at most diagnostic laboratories. We propose a new pipeline, MiDRMpol, to quantify DRM from HIV-1 pol region. The pipeline accepts raw fastq reads as input and output list mutations.