Full-length de novo viral quasispecies assembly through variation graph construction

Baaijens JA, Van der Roest B, Köster J, Stougie L, Schönhuth A (2019)
Bioinformatics 35(24): 5086-5094.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Baaijens, Jasmijn A; Van der Roest, Bastiaan; Köster, Johannes; Stougie, Leen; Schönhuth, AlexanderUniBi
Abstract / Bemerkung
Abstract Motivation Viruses populate their hosts as a viral quasispecies: a collection of genetically related mutant strains. Viral quasispecies assembly is the reconstruction of strain-specific haplotypes from read data, and predicting their relative abundances within the mix of strains is an important step for various treatment-related reasons. Reference genome independent (‘de novo’) approaches have yielded benefits over reference-guided approaches, because reference-induced biases can become overwhelming when dealing with divergent strains. While being very accurate, extant de novo methods only yield rather short contigs. The remaining challenge is to reconstruct full-length haplotypes together with their abundances from such contigs. Results We present Virus-VG as a de novo approach to viral haplotype reconstruction from preassembled contigs. Our method constructs a variation graph from the short input contigs without making use of a reference genome. Then, to obtain paths through the variation graph that reflect the original haplotypes, we solve a minimization problem that yields a selection of maximal-length paths that is, optimal in terms of being compatible with the read coverages computed for the nodes of the variation graph. We output the resulting selection of maximal length paths as the haplotypes, together with their abundances. Benchmarking experiments on challenging simulated and real datasets show significant improvements in assembly contiguity compared to the input contigs, while preserving low error rates compared to the state-of-the-art viral quasispecies assemblers. Availability and implementation Virus-VG is freely available at https://bitbucket.org/jbaaijens/virus-vg. Supplementary information Supplementary data are available at Bioinformatics online.
Stichworte
Statistics and Probability; Computational Theory and Mathematics; Biochemistry; Molecular Biology; Computational Mathematics; Computer Science Applications
Erscheinungsjahr
2019
Zeitschriftentitel
Bioinformatics
Band
35
Ausgabe
24
Seite(n)
5086-5094
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/2941754

Zitieren

Baaijens JA, Van der Roest B, Köster J, Stougie L, Schönhuth A. Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics. 2019;35(24):5086-5094.
Baaijens, J. A., Van der Roest, B., Köster, J., Stougie, L., & Schönhuth, A. (2019). Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics, 35(24), 5086-5094. doi:10.1093/bioinformatics/btz443
Baaijens, J. A., Van der Roest, B., Köster, J., Stougie, L., and Schönhuth, A. (2019). Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics 35, 5086-5094.
Baaijens, J.A., et al., 2019. Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics, 35(24), p 5086-5094.
J.A. Baaijens, et al., “Full-length de novo viral quasispecies assembly through variation graph construction”, Bioinformatics, vol. 35, 2019, pp. 5086-5094.
Baaijens, J.A., Van der Roest, B., Köster, J., Stougie, L., Schönhuth, A.: Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics. 35, 5086-5094 (2019).
Baaijens, Jasmijn A, Van der Roest, Bastiaan, Köster, Johannes, Stougie, Leen, and Schönhuth, Alexander. “Full-length de novo viral quasispecies assembly through variation graph construction”. Bioinformatics 35.24 (2019): 5086-5094.

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