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bioRxiv · 10.1101/2020.02.07.939454

Economic Genome Assembly from Low Coverage Illumina and Nanopore Data

Gatter, T.·von Loehneysen, S.·Drozdova, P.·Hartmann, T.·Stadler, P. F.
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Abstract

We describe a new approach to assemble genomes from a combination of low-coverage short and long reads. LazyBastard starts from a bipartite overlap graph between long reads and restrictively filtered short-read unitigs, which are then reduced to a long-read overlap graph G. Edges are removed from G to obtain first a consistent orientation and then a DAG. Using heuristics based on properties of proper interval graphs, contigs are extracted as maximum weight paths. These are translated into genomic sequence only in the final step. A prototype implementation of LazyBastard, entirely written in python, not only yields significantly more accurate assemblies of the yeast and fruit fly genomes compared to state-of-the-art pipelines but also requires much less computational effort. FundingRSF / Helmholtz Association 18-44-06201; Deutsche Academische Austauschdienst, DFG STA 850/19-2 within SPP 1738; German Federal Ministery of Education an Research 031A538A, de.NBI-RBC

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Gatter, T., von Loehneysen, S., Drozdova, P., Hartmann, T., Stadler, P. F.. 2020-02-08. Economic Genome Assembly from Low Coverage Illumina and Nanopore Data. https://doi.org/10.1101/2020.02.07.939454

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