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

Journal Article · 19 November 2019 · Virus Evolution

DOI: https://doi.org/10.1093/ve/vez050 · OSTI ID:1574552

Araújo, Pedro M. M. ^[1]; Martins, Joana S. ^[1]; Osório, Nuno S.  ^[1]

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1. Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal, ICVS/3B’s - PT Government Associate Laboratory, Braga, Guimarães, Portugal

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.

• Sponsoring Organization: USDOE Office of Nuclear Energy (NE), Nuclear Fuel Cycle and Supply Chain
• Grant/Contract Number: NORTE-01-0145-FEDER-000013; POCI-01-0145-FEDER-007038; IF/00474/2014; PDE/BDE/113599/2015
• OSTI ID: 1574552
• Journal Information: Virus Evolution, Journal Name: Virus Evolution Vol. 5 Journal Issue: 2; ISSN 2057-1577
• Publisher: Oxford University PressCopyright Statement
• Country of Publication: United Kingdom
• Language: English