misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny
As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particul...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Korea Genome Organization
2017-12-01
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| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2017-15-4-128.pdf |
| _version_ | 1818262998525935616 |
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| author | Young-Joon Ko Jung Sun Kim Sangsoo Kim |
| author_facet | Young-Joon Ko Jung Sun Kim Sangsoo Kim |
| author_sort | Young-Joon Ko |
| collection | DOAJ |
| description | As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species. |
| first_indexed | 2024-12-12T19:12:02Z |
| format | Article |
| id | doaj.art-36b6198cbc374f4283115b7bad27b01b |
| institution | Directory Open Access Journal |
| issn | 2234-0742 |
| language | English |
| last_indexed | 2024-12-12T19:12:02Z |
| publishDate | 2017-12-01 |
| publisher | Korea Genome Organization |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj.art-36b6198cbc374f4283115b7bad27b01b2022-12-22T00:14:49ZengKorea Genome OrganizationGenomics & Informatics2234-07422017-12-0115412813510.5808/GI.2017.15.4.128495misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene SyntenyYoung-Joon Ko0Jung Sun Kim1Sangsoo Kim2 Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, KoreaAs next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.http://genominfo.org/upload/pdf/gi-2017-15-4-128.pdfBAC end librarygene syntenygenotyping-by-sequencingmiassemblynext-generation sequencingreference genome |
| spellingShingle | Young-Joon Ko Jung Sun Kim Sangsoo Kim misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny Genomics & Informatics BAC end library gene synteny genotyping-by-sequencing miassembly next-generation sequencing reference genome |
| title | misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny |
| title_full | misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny |
| title_fullStr | misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny |
| title_full_unstemmed | misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny |
| title_short | misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny |
| title_sort | mismm an integrated pipeline for misassembly detection using genotyping by sequencing and its validation with bac end library sequences and gene synteny |
| topic | BAC end library gene synteny genotyping-by-sequencing miassembly next-generation sequencing reference genome |
| url | http://genominfo.org/upload/pdf/gi-2017-15-4-128.pdf |
| work_keys_str_mv | AT youngjoonko mismmanintegratedpipelineformisassemblydetectionusinggenotypingbysequencinganditsvalidationwithbacendlibrarysequencesandgenesynteny AT jungsunkim mismmanintegratedpipelineformisassemblydetectionusinggenotypingbysequencinganditsvalidationwithbacendlibrarysequencesandgenesynteny AT sangsookim mismmanintegratedpipelineformisassemblydetectionusinggenotypingbysequencinganditsvalidationwithbacendlibrarysequencesandgenesynteny |