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VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets
During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determinin...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Cold Spring Harbor Laboratory
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10168208/ https://www.ncbi.nlm.nih.gov/pubmed/37163001 http://dx.doi.org/10.1101/2023.04.25.537842 |
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author | Achouri, Emna Felt, Sébastien A. Hackbart, Matthew Rivera-Espinal, Nicole S. López, Carolina B. |
author_facet | Achouri, Emna Felt, Sébastien A. Hackbart, Matthew Rivera-Espinal, Nicole S. López, Carolina B. |
author_sort | Achouri, Emna |
collection | PubMed |
description | During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years exposing a need for bioinformatic tools that can accurately identify them within Next-Generation Sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm2 (VODKA2), that is optimized to run on a High Performance Computing (HPC) environment for fast and accurate detection of nsVGs from large data sets. |
format | Online Article Text |
id | pubmed-10168208 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-101682082023-05-10 VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets Achouri, Emna Felt, Sébastien A. Hackbart, Matthew Rivera-Espinal, Nicole S. López, Carolina B. bioRxiv Article During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years exposing a need for bioinformatic tools that can accurately identify them within Next-Generation Sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm2 (VODKA2), that is optimized to run on a High Performance Computing (HPC) environment for fast and accurate detection of nsVGs from large data sets. Cold Spring Harbor Laboratory 2023-07-15 /pmc/articles/PMC10168208/ /pubmed/37163001 http://dx.doi.org/10.1101/2023.04.25.537842 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article Achouri, Emna Felt, Sébastien A. Hackbart, Matthew Rivera-Espinal, Nicole S. López, Carolina B. VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets |
title | VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets |
title_full | VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets |
title_fullStr | VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets |
title_full_unstemmed | VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets |
title_short | VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets |
title_sort | vodka2: a fast and accurate method to detect non-standard viral genomes from large rna-seq datasets |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10168208/ https://www.ncbi.nlm.nih.gov/pubmed/37163001 http://dx.doi.org/10.1101/2023.04.25.537842 |
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