Dataset Information

SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing.

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.

SUBMITTER: Araujo PMM

PROVIDER: S-EPMC6863187 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing.

Araújo Pedro M M PMM Martins Joana S JS Osório Nuno S NS

Virus evolution 20190701 2

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 ...[more]

PMID: 31768265

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Dataset Information

SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing.

Publications

SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing.

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