Utilize este identificador para referenciar este registo:
https://hdl.handle.net/1822/67201
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Campo DC | Valor | Idioma |
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dc.contributor.author | Araújo, Pedro Manuel Macedo | por |
dc.contributor.author | Martins, Joana Santos | por |
dc.contributor.author | Osório, Nuno S. | por |
dc.date.accessioned | 2020-10-01T14:25:13Z | - |
dc.date.available | 2020-10-01T14:25:13Z | - |
dc.date.issued | 2019-07 | - |
dc.identifier.citation | Araújo, P. M., Martins, J. S., & Osório, N. S. (2019). SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. Virus evolution, 5(2) | por |
dc.identifier.uri | https://hdl.handle.net/1822/67201 | - |
dc.description.abstract | 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. | por |
dc.description.sponsorship | FEDER, COMPETE, and FCT by the projects NORTE-01-0145-FEDER-000013, POCI-01-0145- FEDER-007038, and IF/00474/2014; FCT PhD scholarship PDE/ BDE/113599/2015; FCT contract IF/00474/2014 | por |
dc.language.iso | eng | por |
dc.publisher | Oxford University Press | por |
dc.rights | openAccess | por |
dc.subject | HIV-1 | por |
dc.subject | subtyping | por |
dc.subject | genetic diversity | por |
dc.subject | scalability | por |
dc.subject | phylogeny | por |
dc.title | SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing | por |
dc.type | article | por |
dc.peerreviewed | yes | por |
oaire.citationIssue | 2 | por |
oaire.citationConferencePlace | https://watermark.silverchair.com/vez050.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAq4wggKqBgkqhkiG9w0BBwagggKbMIIClwIBADCCApAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMxu7DRqXzL-s4N7jZAgEQgIICYdgeqfPriRZFzCTlofOhPONNtCxuKnyydHx9MU8ptL1Sgq59_ltbmPPAAOgTxwcJxBny9M65eGYzyip02x0XHYl0IMgq_QM-3xH-aDFsD6HoBtvV8PJiI89P-jVSgvQvooZmqA9xbmrW1lICBSS0S2auBqSAgTEtes-wElUtHplI4w6b98AjaUv1mOeR6NNcRudzrKbf0vUmiT4oTh5S6gGP-nFMmDjr-t12sDltuxwBfs9DAhi83Sx8vki8P5rk-vHaVJkGjz9gydfAPPtHUBXJhattpxdy6c2HJoZCIHCY98zbiwPAtzxJj_7jLyLJJR-7M-IjA1FMWLtkb4KR92QhKSOpwQni95ne_esIGgkFmLnvuxWDK-DKeAARBVDYHfhQ6BwnzdVhFDGY5nS1Me3a9h_CBUaChUbgKXGgwC-1sQgfwTu5jNSHsBrfsb1Pd9gHU__wq78cmcXjeOACL4wSkIhrRPfhhGFQ17cxrp8KjJzLxIW4Nhtjcbad0mFTiPwYoQboRx25P7pbU74oM2Nww2uNWVUe9sWBi8VMk-WPdy4BoWrP_9tuJaOumkT9aZ7yjRVpLyBBlZSZVBHxfxgfQW_Oa6Na1gWfkhF2T9_zQD8nevEML3qgzRq_fehOwlf-gXqoaT5k4WQL0stHxSmmJAxpwxAkmOJ8zHNcunDjqft0OL2fUq_v0Rk7DtvFnFoM_aiS8FzpyVKCoDPa27ynMo9P21MXAsibi5yQ329bPM8FRNND9gpzn-lp_JfyDaCDe446eSky2kAzip1a3YX0i4mg0BjuxFai_XZ2-VwiWQ | por |
oaire.citationVolume | 5 | por |
dc.identifier.eissn | 2057-1577 | - |
dc.identifier.doi | 10.1093/ve/vez050 | por |
dc.subject.fos | Ciências Médicas::Medicina Básica | por |
dc.subject.wos | Science & Technology | por |
sdum.journal | Virus Evolution | por |
Aparece nas coleções: | ICVS - Artigos em revistas internacionais / Papers in international journals |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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10.1093_ve_vez050.pdf | 278,07 kB | Adobe PDF | Ver/Abrir |