ArticleIn silico biology
QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads.
Article in In silico biology. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding.Molecular biology and evolution · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Article
- Evaluation of haplotype callers for next-generation sequencing of viruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- BHap: a novel approach for bacterial haplotype reconstruction.Bioinformatics (Oxford, England) · 2019Article
- De novo assembly of viral quasispecies using overlap graphs.Genome research · 2017Article
- Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage.Algorithms for molecular biology : AMB · 2016Article
- Inferring the Clonal Structure of Viral Populations from Time Series Sequencing.PLoS computational biology · 2015Article
- Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations.Nucleic acids research · 2015Article
- Accurate viral population assembly from ultra-deep sequencing data.Bioinformatics (Oxford, England) · 2014Article
- Viral quasispecies assembly via maximal clique enumeration.PLoS computational biology · 2014Article
- On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly.BMC bioinformatics · 2014Article
- Viral quasispecies inference from 454 pyrosequencing.BMC bioinformatics · 2013Article
- Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.Scientific reports · 2013Article
- Article
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Authors and funding
5 authors.
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Abstract
Next generation sequencing technologies have recently been applied to characterize mutational spectra of the heterogeneous population of viral genotypes (known as a quasispecies) within HIV-infected patients. Such information is clinically relevant because minority genetic subpopulations of HIV within patients enable viral escape from selection pressures such as the immune response and antiretroviral therapy. However, methods for quasispecies sequence reconstruction from next generation sequencing reads are not yet widely used and remains an emerging area of research. Furthermore, the majority of research methodology in HIV has focused on 454 sequencing, while many next-generation sequencing platforms used in practice are limited to shorter read lengths relative to 454 sequencing. Little work has been done in determining how best to address the read length limitations of other platforms. The approach described here incorporates graph representations of both read differences and read overlap to conservatively determine the regions of the sequence with sufficient variability to separate quasispecies sequences. Within these tractable regions of quasispecies inference, we use constraint programming to solve for an optimal quasispecies subsequence determination via vertex coloring of the conflict graph, a representation which also lends itself to data with non-contiguous reads such as paired-end sequencing. We demonstrate the utility of the method by applying it to simulations based on actual intra-patient clonal HIV-1 sequencing data.
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