Optical map guided genome assembly

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dc.contributor University of Helsinki, Department of Computer Science en
dc.contributor University of Helsinki, Department of Computer Science en
dc.contributor.author Leinonen, Miika
dc.contributor.author Salmela, Leena
dc.date.accessioned 2020-11-05T12:23:01Z
dc.date.available 2020-11-05T12:23:01Z
dc.date.issued 2020-07-06
dc.identifier.citation Leinonen , M & Salmela , L 2020 , ' Optical map guided genome assembly ' , BMC Bioinformatics , vol. 21 , 285 . https://doi.org/10.1186/s12859-020-03623-1 en
dc.identifier.issn 1471-2105
dc.identifier.other PURE: 150523907
dc.identifier.other PURE UUID: f0e45a80-111c-4b77-b1af-8550de210a7f
dc.identifier.other WOS: 000550092500002
dc.identifier.other ORCID: /0000-0002-0756-543X/work/83054581
dc.identifier.uri http://hdl.handle.net/10138/321132
dc.description.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. en
dc.format.extent 19
dc.language.iso eng
dc.relation.ispartof BMC Bioinformatics
dc.rights en
dc.subject Genome assembly en
dc.subject Optical mapping en
dc.subject ALIGNMENT en
dc.subject TOOL en
dc.subject 113 Computer and information sciences en
dc.title Optical map guided genome assembly en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1186/s12859-020-03623-1
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/publishedVersion

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