SARS-CoV-2 survey of reads data and phylogenetic analysis of two datasets
[Description of methods used for collection/generation of data] A worldwide survey using the GISAID EpiCov database was conducted on 2022-06-15, resulting in the collection of a SARS-CoV-2 genome dataset (available via DOI: 10.55876/gis8.230801ex). Another worldwide survey using the ENA database was...
| Autores: | , , , , , , |
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| Tipo de recurso: | conjunto de datos |
| Fecha de publicación: | 2025 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/378670 |
| Acceso en línea: | http://hdl.handle.net/10261/378670 https://doi.org/10.20350/digitalCSIC/17032 |
| Access Level: | acceso abierto |
| Palabra clave: | SARS-CoV-2 Spike Transmission Snakemake |
| Sumario: | [Description of methods used for collection/generation of data] A worldwide survey using the GISAID EpiCov database was conducted on 2022-06-15, resulting in the collection of a SARS-CoV-2 genome dataset (available via DOI: 10.55876/gis8.230801ex). Another worldwide survey using the ENA database was conducted on 2024-12-10. The second survey returned raw reads, and so the code and main processed files are made available here. The "output" folder contains the pipeline output files, including lineage assignment and repaired deletion identification results. Then, transcluster v2.1.0 was run on these datasets. For each dataset, input files containing lists of sample identifiers are contained in the "input" folder. The "output" folder contains the pipeline output files, consisting on a separate folder for each of the input lists, as well as a "summary" folder. Each "config/config.yaml" file describes the pipeline configuration of each run. |
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