Optical map guided genome assembly

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Leinonen , M & Salmela , L 2020 , ' Optical map guided genome assembly ' , BMC Bioinformatics , vol. 21 , 285 . https://doi.org/10.1186/s12859-020-03623-1

Title: Optical map guided genome assembly
Author: Leinonen, Miika; Salmela, Leena
Contributor organization: Department of Computer Science
Algorithmic Bioinformatics
Helsinki Institute for Information Technology
Date: 2020-07-06
Language: eng
Number of pages: 19
Belongs to series: BMC Bioinformatics
ISSN: 1471-2105
DOI: https://doi.org/10.1186/s12859-020-03623-1
URI: http://hdl.handle.net/10138/321132
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 proposeOpticalKermitwhich 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,OpticalKermitproduces an assembly with almost three times higher NGA50 with a lower number of misassemblies on realA. thalianareads. Conclusions OpticalKermitsuccessfully 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
113 Computer and information sciences
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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