{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:31:57Z","timestamp":1772155917073,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,11,19]],"date-time":"2019-11-19T00:00:00Z","timestamp":1574121600000},"content-version":"vor","delay-in-days":141,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002924","name":"FEDER","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002924","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011929","name":"COMPETE","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011929","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["NORTE-01-0145-FEDER-000013"],"award-info":[{"award-number":["NORTE-01-0145-FEDER-000013"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["POCI-01-0145-FEDER-007038"],"award-info":[{"award-number":["POCI-01-0145-FEDER-007038"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["IF\/00474\/2014"],"award-info":[{"award-number":["IF\/00474\/2014"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["PDE\/BDE\/113599\/2015"],"award-info":[{"award-number":["PDE\/BDE\/113599\/2015"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["IF\/00474\/2014"],"award-info":[{"award-number":["IF\/00474\/2014"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Human immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and evolution studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web-servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for large-scale local HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analyzing full-length genomes or partial HIV-1 genomic regions (GAG, POL, and ENV) and recognizes more than ninety circulating recombinant forms. SNAPPy is freely available at: https:\/\/github.com\/PMMAraujo\/snappy\/releases.<\/jats:p>","DOI":"10.1093\/ve\/vez050","type":"journal-article","created":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T07:10:49Z","timestamp":1571382649000},"source":"Crossref","is-referenced-by-count":6,"title":["SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing"],"prefix":"10.1093","volume":"5","author":[{"given":"Pedro M M","family":"Ara\u00fajo","sequence":"first","affiliation":[{"name":"Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal"},{"name":"ICVS\/3B\u2019s - PT Government Associate Laboratory, Braga, Guimar\u00e3es, Portugal"}]},{"given":"Joana S","family":"Martins","sequence":"additional","affiliation":[{"name":"Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal"},{"name":"ICVS\/3B\u2019s - PT Government Associate Laboratory, Braga, Guimar\u00e3es, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0949-5399","authenticated-orcid":false,"given":"Nuno S","family":"Os\u00f3rio","sequence":"additional","affiliation":[{"name":"Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal"},{"name":"ICVS\/3B\u2019s - PT Government Associate Laboratory, Braga, Guimar\u00e3es, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2019,11,19]]},"reference":[{"key":"2019111910004574500_vez050-B1","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1097\/01.aids.0000188422.95162.b7","article-title":"Protease Mutation M89I\/V Is Linked to Therapy Failure in Patients Infected with the HIV-1 non-B Subtypes C, F or G","volume":"19","author":"Abecasis","year":"2005","journal-title":"AIDS"},{"key":"2019111910004574500_vez050-B2","doi-asserted-by":"crossref","first-page":"8543","DOI":"10.1128\/JVI.00463-07","article-title":"Recombination Confounds the Early 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