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

Abstract

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.

Authors:
 [1];  [1]; ORCiD logo [1]
  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
Publication Date:
Sponsoring Org.:
USDOE Office of Nuclear Energy (NE), Fuel Cycle Technologies (NE-5)
OSTI Identifier:
1574552
Grant/Contract Number:  
NORTE-01-0145-FEDER-000013; POCI-01-0145-FEDER-007038; IF/00474/2014; PDE/BDE/113599/2015
Resource Type:
Published Article
Journal Name:
Virus Evolution
Additional Journal Information:
Journal Name: Virus Evolution Journal Volume: 5 Journal Issue: 2; Journal ID: ISSN 2057-1577
Publisher:
Oxford University Press
Country of Publication:
Country unknown/Code not available
Language:
English

Citation Formats

Araújo, Pedro M. M., Martins, Joana S., and Osório, Nuno S. SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. Country unknown/Code not available: N. p., 2019. Web. doi:10.1093/ve/vez050.
Araújo, Pedro M. M., Martins, Joana S., & Osório, Nuno S. SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. Country unknown/Code not available. doi:10.1093/ve/vez050.
Araújo, Pedro M. M., Martins, Joana S., and Osório, Nuno S. Tue . "SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing". Country unknown/Code not available. doi:10.1093/ve/vez050.
@article{osti_1574552,
title = {SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing},
author = {Araújo, Pedro M. M. and Martins, Joana S. and Osório, Nuno S.},
abstractNote = {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.},
doi = {10.1093/ve/vez050},
journal = {Virus Evolution},
number = 2,
volume = 5,
place = {Country unknown/Code not available},
year = {2019},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1093/ve/vez050

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