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Misassembly detection using paired-end sequence reads and optical mapping data.

Muggli MD, Puglisi SJ, Ronen R, Boucher C - Bioinformatics (2015)

Bottom Line: A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes.We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar.Our results demonstrate that we detect more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.

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An example illustrating the red black positional de Bruijn graph (), the positional de Bruijn graph and the de Bruijn graph on a set of aligned reads, with their corresponding sets of k-mers and positional k-mers. There exists a region in the genome that extremely high coverage, which would suggest a possible misassembly error. Namely, the positional k-mers (GCCA, 111), (CCAT, 112) and (CATT, 113) have multiplicity 10, whereas all other positional k-mers have multiplicity 5. In the de Bruijn graph where the position is not taken into account, all k-mers have multiplicity of 10 and there is no evidence of a misassembled region. We note that in this example no vertex gluing operations occur but in more complex instances, vertex gluing will occur when equal k-mers align at adjacent positions
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btv262-F2: An example illustrating the red black positional de Bruijn graph (), the positional de Bruijn graph and the de Bruijn graph on a set of aligned reads, with their corresponding sets of k-mers and positional k-mers. There exists a region in the genome that extremely high coverage, which would suggest a possible misassembly error. Namely, the positional k-mers (GCCA, 111), (CCAT, 112) and (CATT, 113) have multiplicity 10, whereas all other positional k-mers have multiplicity 5. In the de Bruijn graph where the position is not taken into account, all k-mers have multiplicity of 10 and there is no evidence of a misassembled region. We note that in this example no vertex gluing operations occur but in more complex instances, vertex gluing will occur when equal k-mers align at adjacent positions


Misassembly detection using paired-end sequence reads and optical mapping data.

Muggli MD, Puglisi SJ, Ronen R, Boucher C - Bioinformatics (2015)

An example illustrating the red black positional de Bruijn graph (), the positional de Bruijn graph and the de Bruijn graph on a set of aligned reads, with their corresponding sets of k-mers and positional k-mers. There exists a region in the genome that extremely high coverage, which would suggest a possible misassembly error. Namely, the positional k-mers (GCCA, 111), (CCAT, 112) and (CATT, 113) have multiplicity 10, whereas all other positional k-mers have multiplicity 5. In the de Bruijn graph where the position is not taken into account, all k-mers have multiplicity of 10 and there is no evidence of a misassembled region. We note that in this example no vertex gluing operations occur but in more complex instances, vertex gluing will occur when equal k-mers align at adjacent positions
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542784&req=5

btv262-F2: An example illustrating the red black positional de Bruijn graph (), the positional de Bruijn graph and the de Bruijn graph on a set of aligned reads, with their corresponding sets of k-mers and positional k-mers. There exists a region in the genome that extremely high coverage, which would suggest a possible misassembly error. Namely, the positional k-mers (GCCA, 111), (CCAT, 112) and (CATT, 113) have multiplicity 10, whereas all other positional k-mers have multiplicity 5. In the de Bruijn graph where the position is not taken into account, all k-mers have multiplicity of 10 and there is no evidence of a misassembled region. We note that in this example no vertex gluing operations occur but in more complex instances, vertex gluing will occur when equal k-mers align at adjacent positions
Bottom Line: A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes.We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar.Our results demonstrate that we detect more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.

Show MeSH