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Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

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dc.citation.doi10.1186/s12864-015-1911-8
dc.citation.issn1471-2164
dc.citation.jtitleBmc Genomics
dc.citation.spage16
dc.citation.volume16
dc.contributor.authorShelton, J. M.
dc.contributor.authorColeman, M. C.
dc.contributor.authorHemdon, N.
dc.contributor.authorLu, N. Y.
dc.contributor.authorLam, E. T.
dc.contributor.authorAnantharaman, T.
dc.contributor.authorSheth, P.
dc.contributor.authorBrown, Susan J.
dc.contributor.authoreidsjbrown
dc.date.accessioned2016-04-04T22:13:51Z
dc.date.available2016-04-04T22:13:51Z
dc.date.published2015
dc.descriptionCitation: Shelton, J. M., Coleman, M. C., Hemdon, N., Lu, N. Y., Lam, E. T., Anantharaman, T., . . . Brown, S. J. (2015). Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool. Bmc Genomics, 16, 16. doi:10.1186/s12864-015-1911-8
dc.descriptionBackground: Genome assembly remains an unsolved problem. Assembly projects face a range of hurdles that confound assembly. Thus a variety of tools and approaches are needed to improve draft genomes. Results: We used a custom assembly workflow to optimize consensus genome map assembly, resulting in an assembly equal to the estimated length of the Tribolium castaneum genome and with an N50 of more than 1 Mb. We used this map for super scaffolding the T. castaneum sequence assembly, more than tripling its N50 with the program Stitch. Conclusions: In this article we present software that leverages consensus genome maps assembled from extremely long single molecule maps to increase the contiguity of sequence assemblies. We report the results of applying these tools to validate and improve a 7x Sanger draft of the T. castaneum genome.
dc.identifier.urihttp://hdl.handle.net/2097/32245
dc.relation.urihttps://doi.org/10.1186/s12864-015-1911-8
dc.rightsAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectGenome Map
dc.subjectBionano
dc.subjectGenome Scaffolding
dc.subjectGenome Validation
dc.subjectGenome
dc.subjectFinishing
dc.titleTools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool
dc.typeArticle

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