{"id":26572680,"url":"https://github.com/PathoGenOmics-Lab/VIPERA","last_synced_at":"2025-03-23T00:35:31.125Z","repository":{"id":203572583,"uuid":"627797162","full_name":"PathoGenOmics-Lab/VIPERA","owner":"PathoGenOmics-Lab","description":"A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis","archived":false,"fork":false,"pushed_at":"2025-03-06T17:03:00.000Z","size":7145,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-06T17:31:27.338Z","etag":null,"topics":["bioinformatics","intrahost","reporting","sars-cov-2","snakemake","virus-evolution"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PathoGenOmics-Lab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-04-14T08:13:21.000Z","updated_at":"2025-01-28T10:07:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"6cb65a9d-2a15-4e11-b61a-cc33f75b605e","html_url":"https://github.com/PathoGenOmics-Lab/VIPERA","commit_stats":{"total_commits":390,"total_committers":6,"mean_commits":65.0,"dds":0.441025641025641,"last_synced_commit":"dd355717cdbe427772b70807db2ecf8b4f4c4447"},"previous_names":["pathogenomics-lab/vipera"],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PathoGenOmics-Lab%2FVIPERA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PathoGenOmics-Lab%2FVIPERA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PathoGenOmics-Lab%2FVIPERA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PathoGenOmics-Lab%2FVIPERA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PathoGenOmics-Lab","download_url":"https://codeload.github.com/PathoGenOmics-Lab/VIPERA/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245040215,"owners_count":20551297,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","intrahost","reporting","sars-cov-2","snakemake","virus-evolution"],"created_at":"2025-03-23T00:34:37.839Z","updated_at":"2025-03-23T00:35:31.111Z","avatar_url":"https://github.com/PathoGenOmics-Lab.png","language":"Python","funding_links":[],"categories":["Functional Analysis"],"sub_categories":["Evolutionary Analysis"],"readme":"# VIPERA\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"logo.jpg\" title=\"VIPERA logo\"\u003e\n\u003c/p\u003e\n\n[![PGO badge](https://img.shields.io/badge/PathoGenOmics-Lab-yellow.svg)](https://pathogenomics.github.io/)\n[![DOI](https://img.shields.io/badge/Virus_Evolution-10.1093/ve/veae018-387088.svg)](https://doi.org/10.1093/ve/veae018)\n[![Release](https://img.shields.io/github/v/release/PathoGenOmics-Lab/VIPERA)](https://github.com/PathoGenOmics-Lab/VIPERA/releases)\n[![Snakemake](https://img.shields.io/badge/Snakemake-≥7.19-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)\n![Install workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/install.yml/badge.svg)\n![Test workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test.yml/badge.svg)\n\nA pipeline for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis.\n\n## First steps\n\nTo run VIPERA locally with the default configuration, you only need one line of code after\n[installing Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html),\nconfiguring [the inputs and outputs](config/README.md#inputs-and-outputs) and\n[the context dataset](config/README.md#automated-construction-of-a-context-dataset):\n\n```shell\nsnakemake --use-conda -c4  # runs VIPERA on 4 cores\n```\n\nWe 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)\nand performs the analysis in a single step:\n\n```shell\n./run_default_VIPERA.sh\n```\n\nThis Snakemake workflow is compatible with both local execution and HPC environments utilizing SLURM. It supports dependency management through either conda or Singularity, as detailed in the [run modes documentation](config/README.md#run-modes).\n\nPlease refer to the [full workflow documentation](config/README.md) for detailed setup instructions.\n\n\u003e The documentation in this repository provides instructions for running VIPERA\n\u003e with Snakemake \u003c8. We recommend using Snakemake 7.32.\n\u003e However, using Snakemake 8 is possible with minimal modifications (see the\n\u003e [migration documentation](https://snakemake.readthedocs.io/en/stable/getting_started/migration.html)).\n\u003e For example, `--use-conda` and `--use-singularity` are deprecated in Snakemake 8,\n\u003e and `--software-deployment-method conda apptainer` is the preferred way to provide the options. Additionally, SLURM support is only available after installing an\n\u003e [executor plugin for slurm](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html).\n\n## Contributors\n\n[![Contributors figure](https://contrib.rocks/image?repo=PathoGenOmics-Lab/VIPERA)](https://github.com/PathoGenOmics-Lab/VIPERA/graphs/contributors)\n\n## Citation\n\n\u003e Álvarez-Herrera, M. \u0026 Sevilla, J., Ruiz-Rodriguez, P., Vergara, A., Vila, J., Cano-Jiménez, P., González-Candelas, F., Comas, I., \u0026 Coscollá, M. (2024). VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus Evolution, 10(1), veae018. https://doi.org/10.1093/ve/veae018\n\n```bibtex\n@article{ahs2024,\n  title = {{VIPERA}: {Viral} {Intra}-{Patient} {Evolution} {Reporting} and {Analysis}},\n  volume = {10},\n  issn = {2057-1577},\n  shorttitle = {{VIPERA}},\n  url = {https://doi.org/10.1093/ve/veae018},\n  doi = {10.1093/ve/veae018},\n  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.},\n  number = {1},\n  journal = {Virus Evolution},\n  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},\n  month = jan,\n  year = {2024},\n  pages = {veae018},\n  note = {$^*$ indicates equal contribution}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FPathoGenOmics-Lab%2FVIPERA","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FPathoGenOmics-Lab%2FVIPERA","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FPathoGenOmics-Lab%2FVIPERA/lists"}