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]
- 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), Nuclear Fuel Cycle and Supply Chain
- 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:
- United Kingdom
- 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. United Kingdom: 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. United Kingdom. https://doi.org/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". United Kingdom. https://doi.org/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 = {United Kingdom},
year = {Tue Nov 19 00:00:00 EST 2019},
month = {Tue Nov 19 00:00:00 EST 2019}
}
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