ArticleGenome biology2022
VirStrain: a strain identification tool for RNA viruses.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- Evolutionary patterns of pH1N1 and H3N2 in relation to vaccine use.BMC genomics · 2026Article
- Evaluation of targeted next-generation sequencing for detection of HPV genotypes and sublineages in cervical liquid-based cytology SurePath samples from the Danish screening program.International journal of cancer · 2026Article
- Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.Microbial genomics · 2026Article
- A Computational Pipeline for the Identification of RNA Virome in Legumes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance.Bioinformatics (Oxford, England) · 2025Article
- BonoboFlow: viral genome assembly and haplotype reconstruction from nanopore reads.Bioinformatics advances · 2025Article
- Experimental co-infection of calves with SARS-CoV-2 Delta and Omicron variants of concern.Emerging microbes & infections · 2024Article
- VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.Molecular biology and evolution · 2024Article
- Article
- A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes.BMC genomics · 2023Article
- High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs.GigaScience · 2022Article
- The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.Scientific reports · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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