Browsing by Author "Ssekagiri, Alfred"

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    QuasiFlow: A Nextflow Pipeline for Analysis of NGS-based HIV-1 Drug Resistance Data
    (Bioinformatics advances, 2022) Ssekagiri, Alfred; Jjingo, Daudi; Lujumba, Ibra; Bbosa, Nicholas; Bugembe, Daniel L.; Kateete, David P.; Kaleebu, Pontiano; Ssemwanga, Deogratius
    Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the tools for analyzing HIV-1 drug resistance (HIVDR) testing data are mostly web-based which requires uploading data to webservers. This is a challenge for laboratories with internet connectivity issues and instances with restricted data transfer across networks. We present QuasiFlow, a pipeline for reproducible analysis of NGS-based HIVDR testing data across different computing environments. Since QuasiFlow entirely depends on command-line tools and a local copy of the reference database, it eliminates challenges associated with uploading HIV-1 NGS data onto webservers. The pipeline takes raw sequence reads in FASTQ format as input and generates a user-friendly report in PDF/HTML format. The drug resistance scores obtained using QuasiFlow were 100% and 99.12% identical to those obtained using web-based HIVdb program and HyDRA web respectively at a mutation detection threshold of 20%.