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Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs

Abstract : The goal of haplotype-aware genome assembly is to reconstruct all individual haplotypes from a mixed sample and to provide corresponding abundance estimates. We provide a reference-genome-independent solution based on the construction of a variation graph, capturing all diversity present in the sample. We solve the contig abundance estimation problem and propose a greedy algorithm to efficiently build maximal-length haplotypes. Finally, we obtain accurate frequency estimates for the reconstructed haplotypes through linear programming techniques. Our method outperforms state-of-the-art approaches on viral quasispecies benchmarks and has the potential to assemble bacterial genomes in a strain-aware manner as well.
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https://hal.inria.fr/hal-02955692
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Submitted on : Friday, October 2, 2020 - 10:44:19 AM
Last modification on : Saturday, October 3, 2020 - 4:07:27 AM

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Jasmijn Baaijens, Leen Stougie, Alexander Schönhuth. Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs. International Conference on Research in Computational Molecular Biology (RECOMB 2020), 2020, Padova (Virtual), Italy. pp.221-222, ⟨10.1007/978-3-030-45257-5_14⟩. ⟨hal-02955692⟩

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