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https://hdl.handle.net/1822/67201
Título: | SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing |
Autor(es): | Araújo, Pedro Manuel Macedo Martins, Joana Santos Osório, Nuno S. |
Palavras-chave: | HIV-1 subtyping genetic diversity scalability phylogeny |
Data: | Jul-2019 |
Editora: | Oxford University Press |
Revista: | Virus Evolution |
Citação: | 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) |
Resumo(s): | 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. |
Tipo: | Artigo |
URI: | https://hdl.handle.net/1822/67201 |
DOI: | 10.1093/ve/vez050 |
e-ISSN: | 2057-1577 |
Arbitragem científica: | yes |
Acesso: | Acesso aberto |
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 |