VirStrain : a strain identification tool for RNA viruses
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Author(s)
Related Research Unit(s)
Detail(s)
Original language | English |
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Article number | 38 |
Journal / Publication | Genome Biology |
Volume | 23 |
Issue number | 1 |
Online published | 31 Jan 2022 |
Publication status | Published - 2022 |
Link(s)
DOI | DOI |
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Attachment(s) | Documents
Publisher's Copyright Statement
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Link to Scopus | https://www.scopus.com/record/display.uri?eid=2-s2.0-85123973419&origin=recordpage |
Permanent Link | https://scholars.cityu.edu.hk/en/publications/publication(b2137cd5-f2e3-4d79-b595-88beecf4a20d).html |
Abstract
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.
Research Area(s)
- RNA virus, Strain-level analysis, k-mer
Citation Format(s)
VirStrain: a strain identification tool for RNA viruses. / Liao, Herui; Cai, Dehan; Sun, Yanni.
In: Genome Biology, Vol. 23, No. 1, 38, 2022.
In: Genome Biology, Vol. 23, No. 1, 38, 2022.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
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