Optical map guided genome assembly

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BMC Bioinformatics. 2020 Jul 06;21(1):285

Title: Optical map guided genome assembly
Author: Leinonen, Miika; Salmela, Leena
Publisher: BioMed Central
Date: 2020-07-06
URI: http://hdl.handle.net/10138/317676
Abstract: Abstract Background The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly. Results We propose OpticalKermit which directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler, OpticalKermit produces an assembly with almost three times higher NGA50 with a lower number of misassemblies on real A. thaliana reads. Conclusions OpticalKermit successfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.
Subject: Genome assembly
Optical mapping

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