CITATION.cff

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cff-version: 1.2.0
title: VIPERA
message: >-
  If you use this software, please cite it using the
  metadata in this file and the associated publication.
type: software
authors:
  - given-names: Miguel
    family-names: Álvarez-Herrera
    email: m.alvarez.herrera@csic.es
    affiliation: >-
      PathoGenOmics Lab, Institute for Integrative Systems
      Biology (I2SysBio, University of Valencia - CSIC),
      FISABIO Joint Research Unit “Infection and Public
      Health”, Paterna, Spain
    orcid: 'https://orcid.org/0000-0002-7922-3180'
  - given-names: Jordi
    family-names: Sevilla
    affiliation: >-
      PathoGenOmics Lab, Institute for Integrative Systems
      Biology (I2SysBio, University of Valencia - CSIC),
      FISABIO Joint Research Unit “Infection and Public
      Health”, Paterna, Spain
    orcid: 'https://orcid.org/0009-0001-3352-1537'
    email: jordisevilla2001@gmail.com
  - given-names: Paula
    family-names: Ruiz-Rodríguez
    email: paula.ruiz-rodriguez@uv.es
    affiliation: >-
      PathoGenOmics Lab, Institute for Integrative Systems
      Biology (I2SysBio, University of Valencia - CSIC),
      FISABIO Joint Research Unit “Infection and Public
      Health”, Paterna, Spain
    orcid: 'https://orcid.org/0000-0003-0727-5974'
  - given-names: Andrea
    family-names: Vergara
    email: vergara@clinic.cat
    orcid: 'https://orcid.org/0000-0002-5046-4490'
    affiliation: >-
      Department of Clinical Microbiology, CDB, Hospital
      Clínic of Barcelona; University of Barcelona;
      ISGlobal, Barcelona, Spain; CIBER of Infectious
      Diseases (CIBERINFEC), Madrid, Spain
  - given-names: Jordi
    family-names: Vila
    email: jvila@clinic.cat
    orcid: 'https://orcid.org/0000-0002-8025-3926'
    affiliation: >-
      Department of Clinical Microbiology, CDB, Hospital
      Clínic of Barcelona; University of Barcelona;
      ISGlobal, Barcelona, Spain; CIBER of Infectious
      Diseases (CIBERINFEC), Madrid, Spain
  - given-names: Pablo
    family-names: Cano-Jiménez
    email: pcano@ibv.csic.es
    orcid: 'https://orcid.org/0009-0007-4773-3198'
    affiliation: >-
      Institute of Biomedicine of Valencia (IBV-CSIC),
      Valencia, Spain
  - given-names: Fernando
    family-names: González-Candelas
    email: fernando.gonzalez@uv.es
    orcid: 'https://orcid.org/0000-0002-0879-5798'
    affiliation: >-
      Institute for Integrative Systems Biology (I2SysBio,
      University of Valencia - CSIC), FISABIO Joint Research
      Unit “Infection and Public Health”, Paterna, Spain;
      CIBER of Epidemiology and Public Health (CIBERESP),
      Madrid, Spain
  - given-names: Iñaki
    family-names: Comas
    affiliation: >-
      Institute of Biomedicine of Valencia (IBV-CSIC),
      Valencia, Spain; CIBER of Epidemiology and Public
      Health (CIBERESP), Madrid, Spain
    orcid: 'https://orcid.org/0000-0001-5504-9408'
    email: icomas@ibv.csic.es
  - given-names: Mireia
    family-names: Coscolla
    email: mireia.coscolla@uv.es
    orcid: 'https://orcid.org/0000-0003-0752-0538'
    affiliation: >-
      Institute for Integrative Systems Biology (I2SysBio,
      University of Valencia - CSIC), FISABIO Joint Research
      Unit “Infection and Public Health”, Paterna, Spain
identifiers:
  - type: doi
    value: 10.1093/ve/veae018
    description: Journal article
  - type: doi
    value: 10.20350/digitalCSIC/15648
    description: >-
      Case study data: SARS-CoV-2 mapped reads and consensus
      genomes of an intra-patient serially sampled infection
repository-code: 'https://github.com/PathoGenOmics-Lab/VIPERA'
url: 'https://doi.org/10.1093/ve/veae018'
abstract: >-
  Viral mutations within patients nurture the adaptive
  potential of severe acute respiratory syndrome coronavirus
  2 (SARS-CoV-2) during chronic infections, which are a
  potential source of variants of concern. However, there is
  no integrated framework for the evolutionary analysis of
  intra-patient SARS-CoV-2 serial samples. Herein, we
  describe Viral Intra-Patient Evolution Reporting and
  Analysis (VIPERA), a new software that integrates the
  evaluation of the intra-patient ancestry of SARS-CoV-2
  sequences with the analysis of evolutionary trajectories
  of serial sequences from the same viral infection. We have
  validated it using positive and negative control datasets
  and have successfully applied it to a new case, which
  revealed population dynamics and evidence of adaptive
  evolution. VIPERA is available under a free software
  license at https://github.com/PathoGenOmics-Lab/VIPERA.
keywords:
  - SARS-CoV-2
  - Intra-host viral evolution
  - Chronic infection
  - Bioinformatics
  - Snakemake
license: GPL-3.0
version: 1.2.0