{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T13:07:38Z","timestamp":1791464858738,"version":"4.3.4"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000},"content-version":"vor","delay-in-days":331,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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%.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>QuasiFlow and corresponding documentation are publicly available at https:\/\/github.com\/AlfredUg\/QuasiFlow. The pipeline is implemented in Nextflow and requires regular updating of the Stanford HIV drug resistance interpretation algorithm.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics Advances online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbac089","type":"journal-article","created":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T23:01:52Z","timestamp":1669330912000},"source":"Crossref","is-referenced-by-count":5,"title":["QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data"],"prefix":"10.1093","volume":"2","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6549-3550","authenticated-orcid":false,"given":"Alfred","family":"Ssekagiri","sequence":"first","affiliation":[{"name":"Department of General Virology, Uganda Virus Research Institute , Entebbe 31405, Uganda"},{"name":"Department of Immunology and Molecular Biology, Makerere University , Kampala 10206, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daudi","family":"Jjingo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Makerere University , Kampala 10207, Uganda"},{"name":"African Center of Excellence in Bioinformatics and Data Intensive Sciences, Makerere University , Kampala 10207, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibra","family":"Lujumba","sequence":"additional","affiliation":[{"name":"Department of Immunology and Molecular Biology, Makerere University , Kampala 10206, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Bbosa","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit , Entebbe 31405, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel L","family":"Bugembe","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit , Entebbe 31405, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David P","family":"Kateete","sequence":"additional","affiliation":[{"name":"Department of Immunology and Molecular Biology, Makerere University , Kampala 10206, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4996-2203","authenticated-orcid":false,"given":"I King","family":"Jordan","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pontiano","family":"Kaleebu","sequence":"additional","affiliation":[{"name":"Department of General Virology, Uganda Virus Research Institute , Entebbe 31405, Uganda"},{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit , Entebbe 31405, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9675-4234","authenticated-orcid":false,"given":"Deogratius","family":"Ssemwanga","sequence":"additional","affiliation":[{"name":"Department of General Virology, Uganda Virus Research Institute , Entebbe 31405, Uganda"},{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit , Entebbe 31405, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,28]]},"reference":[{"key":"2022120520450824300_vbac089-B2","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2022120520450824300_vbac089-B3","doi-asserted-by":"crossref","first-page":"1186","DOI":"10.21105\/joss.01186","article-title":"Sierra-local: a lightweight standalone application for drug resistance prediction","volume":"4","author":"Ho","year":"2019","journal-title":"Softw. J. Open Source Softw"},{"key":"2022120520450824300_vbac089-B4","doi-asserted-by":"crossref","first-page":"e25193","DOI":"10.1002\/jia2.25193","article-title":"Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the winnipeg consensus","volume":"21","author":"Ji","year":"2018","journal-title":"J. Intern. AIDS Soc"},{"key":"2022120520450824300_vbac089-B5","doi-asserted-by":"crossref","first-page":"586","DOI":"10.3390\/v12060586","article-title":"Are we ready for NGS HIV drug resistance testing? The second \u201cwinnipeg consensus\u201d symposium","volume":"12","author":"Ji","year":"2020","journal-title":"Viruses"},{"key":"2022120520450824300_vbac089-B6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/BIB\/BBAB399","article-title":"Bioinformatics mentorship in a resource limited setting","volume":"23","author":"Jjingo","year":"2022","journal-title":"Brief. 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Dis"},{"key":"2022120520450824300_vbac089-B15","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1093\/jac\/dky561","article-title":"Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes","volume":"74","author":"Su","year":"2019","journal-title":"J. Antimicrob. Chemother"},{"key":"2022120520450824300_vbac089-B16","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat. 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