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

Baaijens JA, Van der Roest B, Köster J, Stougie L, Schönhuth A (2018)
bioRxiv.

Preprint | Veröffentlicht | Englisch
 
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Autor*in
Baaijens, Jasmijn A.; Van der Roest, Bastiaan; Köster, Johannes; Stougie, Leen; Schönhuth, AlexanderUniBi
Abstract / Bemerkung
AbstractMotivationViruses populate their hosts as a viral quasispecies: a collection of genetically related mutant strains. Viral quasispecies assembly refers to reconstructing the strain-specific haplotypes from read data, and predicting their relative abundances within the mix of strains, 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. It remains to reconstruct full-length haplotypes together with their abundances from such contigs.MethodWe first construct a variation graph, a recently popular, suitable structure for arranging and integrating several related genomes, from the short input contigs, without making use of a reference genome. 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.ResultsBenchmarking experiments on challenging simulated data sets show significant improvements in assembly contiguity compared to the input contigs, while preserving low error rates. As a consequence, our method outperforms all state-of-the-art viral quasispecies assemblers that aim at the construction of full-length haplotypes, in terms of various relevant assembly measures. Our tool, Virus-VG, is publicly available at https://bitbucket.org/jbaaijens/virus-vg.
Erscheinungsjahr
2018
Zeitschriftentitel
bioRxiv
Page URI
https://pub.uni-bielefeld.de/record/2941767

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Baaijens JA, Van der Roest B, Köster J, Stougie L, Schönhuth A. Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv. 2018.
Baaijens, J. A., Van der Roest, B., Köster, J., Stougie, L., & Schönhuth, A. (2018). Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv
Baaijens, J. A., Van der Roest, B., Köster, J., Stougie, L., and Schönhuth, A. (2018). Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv.
Baaijens, J.A., et al., 2018. Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv.
J.A. Baaijens, et al., “Full-length de novo viral quasispecies assembly through variation graph construction”, bioRxiv, 2018.
Baaijens, J.A., Van der Roest, B., Köster, J., Stougie, L., Schönhuth, A.: Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv. (2018).
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”. bioRxiv (2018).

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Preprint: 10.1101/287177

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