vipera
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
Science Score: 57.0%
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Low similarity (13.4%) to scientific vocabulary
Keywords
Repository
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
Basic Info
Statistics
- Stars: 6
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 5
Topics
Metadata Files
README.md
VIPERA
A pipeline for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis.
First steps
To run VIPERA locally with the default configuration, you only need one line of code after installing Snakemake, configuring the inputs and outputs and the context dataset:
shell
snakemake --use-conda --cores 4 # command for Snakemake v7
We provide a simple script that downloads the data from our study and performs the analysis in a single step:
shell
./run_default_VIPERA.sh
The workflow is compatible with both local execution and HPC environments utilizing SLURM. The latter requires installing the Snakemake executor plugin for SLURM. It supports dependency management through either conda or Apptainer/Singularity, as detailed in the run modes documentation.
We use continuous integration (CI) to automatically verify that all dependencies install correctly
with Snakemake v7.32.4 (see GitHub Action Install), and to test that VIPERA runs
successfully with Snakemake v7.32.4, v8.30.0, and v9.1.6 using conda (Actions Test Sm v[7-9]).
We also test a containerized workflow with Snakemake v9.1.6 and Apptainer using a
remote image (Action Test Sm v9 Apptainer).
This image is automatically updated in every version (Action Deploy).
Please refer to the full workflow documentation for detailed instructions.
Contributors
Citation
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
@article{ahs2024,
title = {{VIPERA}: {Viral} {Intra}-{Patient} {Evolution} {Reporting} and {Analysis}},
volume = {10},
issn = {2057-1577},
shorttitle = {{VIPERA}},
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}
}
Owner
- Name: PathoGenOmics Lab
- Login: PathoGenOmics-Lab
- Kind: organization
- Location: Spain
- Website: https://www.uv.es/pathogenomic
- Twitter: gen_UV
- Repositories: 1
- Profile: https://github.com/PathoGenOmics-Lab
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
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
GitHub Events
Total
- Release event: 2
- Watch event: 2
- Delete event: 11
- Push event: 82
- Create event: 12
Last Year
- Release event: 2
- Watch event: 2
- Delete event: 11
- Push event: 82
- Create event: 12
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Miguel Álvarez Herrera | m****a@c****s | 218 |
| Jordi Sevilla | j****1@g****m | 162 |
| = | = | 5 |
| Jordi Sevilla Fortuny | 1****i | 2 |
| Miguel | a****g | 2 |
| Jordi Sevilla jorsefor@alumni.uv.es | j****r@m****d | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 2 years ago
All Time
- Total issues: 1
- Total pull requests: 21
- Average time to close issues: about 9 hours
- Average time to close pull requests: 2 days
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.14
- Merged pull requests: 21
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 21
- Average time to close issues: about 9 hours
- Average time to close pull requests: 2 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.14
- Merged pull requests: 21
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Paururo (1)
Pull Request Authors
- SeviJordi (11)
- ahmig (10)