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Economic Genome Assembly from Low Coverage Illumina and Nanopore Data

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

2020-02-08 bioinformatics
10.1101/2020.02.07.939454 bioRxiv
Show 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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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.