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

Pedro M.M. Araújo, Joana S. Martins, View ORCID ProfileNuno S. Osório
doi: https://doi.org/10.1101/725838
Pedro M.M. Araújo
1Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
2ICVS/3B’s - PT Government Associate Laboratory, Braga, Guimarães, Portugal
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Joana S. Martins
1Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
2ICVS/3B’s - PT Government Associate Laboratory, Braga, Guimarães, Portugal
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Nuno S. Osório
1Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
2ICVS/3B’s - PT Government Associate Laboratory, Braga, Guimarães, Portugal
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  • ORCID record for Nuno S. Osório
  • For correspondence: nosorio@med.uminho.pt
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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 surveillance 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 local and high-throughput 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 analysing full-length genomes or partial HIV-1 genomic regions (GAG, POL, ENV) and recognizes more than 90 circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy.

Footnotes

  • https://snappy-hiv1-subtyping.readthedocs.io/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 05, 2019.
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SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing
Pedro M.M. Araújo, Joana S. Martins, Nuno S. Osório
bioRxiv 725838; doi: https://doi.org/10.1101/725838
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SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing
Pedro M.M. Araújo, Joana S. Martins, Nuno S. Osório
bioRxiv 725838; doi: https://doi.org/10.1101/725838

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