Update publication

CITATION.cff

@@ -88,35 +88,37 @@ authors:
       Unit “Infection and Public Health”, Paterna, Spain
 identifiers:
   - type: doi
-    value: 10.1101/2023.10.24.561010
-    description: Preprint
+    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/10.1101/2023.10.24.561010'
+url: 'https://doi.org/10.1093/ve/veae018'
 abstract: >-
   Viral mutations within patients nurture the adaptive
-  potential of 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 intrapatient SARS-CoV-2 serial samples. Herein
-  we describe VIPERA (Viral Intra-Patient Evolution
-  Reporting and Analysis), a new software that integrates
-  the evaluation of the intra-patient ancestry of SARS-CoV-2
+  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, thus
-  enabling an easy and automatic analysis of intra-patient
-  SARS-CoV-2 sequences.
+  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: 1.0.0
+version: 1.2.0

README.md

@@ -5,7 +5,7 @@
 </p>
 
 [![PGO badge](https://img.shields.io/badge/PathoGenOmics-Lab-yellow.svg)](https://pathogenomics.github.io/)
-[![DOI:10.1101/2023.10.24.561010](https://img.shields.io/badge/DOI-10.1101/2023.10.24.561010-blue.svg)](https://doi.org/10.1101/2023.10.24.561010)
+[![DOI](https://img.shields.io/badge/Virus_Evolution-10.1093/ve/veae018-387088.svg)](https://doi.org/10.1093/ve/veae018)
 [![Release](https://img.shields.io/github/v/release/PathoGenOmics-Lab/VIPERA)](https://github.com/PathoGenOmics-Lab/VIPERA/releases)
 [![Snakemake](https://img.shields.io/badge/Snakemake-≥7.19-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)
 ![Install workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/install.yml/badge.svg)
@@ -24,7 +24,7 @@ configuring [the inputs and outputs](config/README.md#inputs-and-outputs) and
 snakemake --use-conda -c4  # runs VIPERA on 4 cores
 ```
 
-We provide a simple script that downloads the [data](https://doi.org/10.20350/digitalCSIC/15648) from [our study](https://doi.org/10.1101/2023.10.24.561010)
+We provide a simple script that downloads the [data](https://doi.org/10.20350/digitalCSIC/15648) from [our study](https://doi.org/10.1093/ve/veae018)
 and performs the analysis in a single step:
 
 ```shell
@@ -49,18 +49,23 @@ Please refer to the [full workflow documentation](config/README.md) for detailed
 
 ## Citation
 
-Álvarez-Herrera M. & Sevilla, J., Ruiz-Rodriguez, P., Vergara, A., Vila, J., Cano-Jiménez, P., González-Candelas, F., Comas, I., & Coscolla, M. (2023). VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. bioRxiv. https://doi.org/10.1101/2023.10.24.561010
+> Álvarez-Herrera, M. & Sevilla, J., Ruiz-Rodriguez, P., Vergara, A., Vila, J., Cano-Jiménez, P., González-Candelas, F., Comas, I., & Coscollá, M. (2024). VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus Evolution, 10(1), veae018. https://doi.org/10.1093/ve/veae018
 
 ```bibtex
-@misc{AHS_VIPERA_2023,
+@article{alvarez-herrera_vipera_2024,
   title = {{VIPERA}: {Viral} {Intra}-{Patient} {Evolution} {Reporting} and {Analysis}},
+  volume = {10},
+  issn = {2057-1577},
   shorttitle = {{VIPERA}},
-  author = {Álvarez-Herrera$^*$, Miguel and Sevilla$^*$, Jordi and Ruiz-Rodriguez, Paula and Vergara, Andrea and Vila, Jordi and Cano-Jiménez, Pablo and González-Candelas, Fernando and Comas, Iñaki and Coscolla, Mireia},
-  url = {https://www.biorxiv.org/content/10.1101/2023.10.24.561010},
-  doi = {10.1101/2023.10.24.561010},
-  language = {en},
-  urldate = {2023-10-25},
-  publisher = {bioRxiv},
+  url = {https://doi.org/10.1093/ve/veae018},
+  doi = {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.},
+  number = {1},
+  journal = {Virus Evolution},
+  author = {Álvarez-Herrera$^*$, Miguel and Sevilla$^*$, Jordi and Ruiz-Rodriguez, Paula and Vergara, Andrea and Vila, Jordi and Cano-Jiménez, Pablo and González-Candelas, Fernando and Comas, Iñaki and Coscollá, Mireia},
+  month = jan,
+  year = {2024},
+  pages = {veae018},
   note = {$^*$ indicates equal contribution}
 }
 ```