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VirStrain: a strain identification tool for RNA viruses
Viruses change constantly during replication, leading to high intra-species diversity. Although many changes are neutral or deleterious, some can confer on the virus different biological properties such as better adaptability. In addition, viral genotypes often have associated metadata, such as host...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8801933/ https://www.ncbi.nlm.nih.gov/pubmed/35101081 http://dx.doi.org/10.1186/s13059-022-02609-x |
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author | Liao, Herui Cai, Dehan Sun, Yanni |
author_facet | Liao, Herui Cai, Dehan Sun, Yanni |
author_sort | Liao, Herui |
collection | PubMed |
description | Viruses change constantly during replication, leading to high intra-species diversity. Although many changes are neutral or deleterious, some can confer on the virus different biological properties such as better adaptability. In addition, viral genotypes often have associated metadata, such as host residence, which can help with inferring viral transmission during pandemics. Thus, subspecies analysis can provide important insights into virus characterization. Here, we present VirStrain, a tool taking short reads as input with viral strain composition as output. We rigorously test VirStrain on multiple simulated and real virus sequencing datasets. VirStrain outperforms the state-of-the-art tools in both sensitivity and accuracy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-022-02609-x). |
format | Online Article Text |
id | pubmed-8801933 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-88019332022-01-31 VirStrain: a strain identification tool for RNA viruses Liao, Herui Cai, Dehan Sun, Yanni Genome Biol Method Viruses change constantly during replication, leading to high intra-species diversity. Although many changes are neutral or deleterious, some can confer on the virus different biological properties such as better adaptability. In addition, viral genotypes often have associated metadata, such as host residence, which can help with inferring viral transmission during pandemics. Thus, subspecies analysis can provide important insights into virus characterization. Here, we present VirStrain, a tool taking short reads as input with viral strain composition as output. We rigorously test VirStrain on multiple simulated and real virus sequencing datasets. VirStrain outperforms the state-of-the-art tools in both sensitivity and accuracy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-022-02609-x). BioMed Central 2022-01-31 /pmc/articles/PMC8801933/ /pubmed/35101081 http://dx.doi.org/10.1186/s13059-022-02609-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Method Liao, Herui Cai, Dehan Sun, Yanni VirStrain: a strain identification tool for RNA viruses |
title | VirStrain: a strain identification tool for RNA viruses |
title_full | VirStrain: a strain identification tool for RNA viruses |
title_fullStr | VirStrain: a strain identification tool for RNA viruses |
title_full_unstemmed | VirStrain: a strain identification tool for RNA viruses |
title_short | VirStrain: a strain identification tool for RNA viruses |
title_sort | virstrain: a strain identification tool for rna viruses |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8801933/ https://www.ncbi.nlm.nih.gov/pubmed/35101081 http://dx.doi.org/10.1186/s13059-022-02609-x |
work_keys_str_mv | AT liaoherui virstrainastrainidentificationtoolforrnaviruses AT caidehan virstrainastrainidentificationtoolforrnaviruses AT sunyanni virstrainastrainidentificationtoolforrnaviruses |