A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs

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dc.contributor.authorLiu, Mingmingen
dc.contributor.authorAdelman, Zach N.en
dc.contributor.authorMyles, Kevin M.en
dc.contributor.authorZhang, Liqingen
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2019-05-20T11:48:10Zen
dc.date.available2019-05-20T11:48:10Zen
dc.date.issued2014-05-28en
dc.date.updated2019-05-20T06:51:19Zen
dc.description.abstractWith the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. Sequence assembly approaches have been modified to meet the requirements for de novo transcriptomes, which have complications not found in traditional genome assemblies such as variation in coverage for each candidate mRNA and alternative splicing. As a consequence, de novo assembly strategies tend to generate a large number of redundant contigs due to sequence variations, which adversely affects downstream analysis and experiments. In this work we proposed TransPS, a transcriptome post-scaffolding method, to generate high quality, nonredundant de novo transcriptomes. TransPS shows promising results on the test transcriptome datasets, where redundancy is greatly reduced by more than 50% and, at the same time, coverage is improved considerably. The web server and source code are available.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationMingming Liu, Zach N. Adelman, Kevin M. Myles, and Liqing Zhang, “A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs,” Computational Biology Journal, vol. 2014, Article ID 961823, 4 pages, 2014. doi:10.1155/2014/961823en
dc.identifier.doihttps://doi.org/10.1155/2014/961823en
dc.identifier.urihttp://hdl.handle.net/10919/89571en
dc.language.isoenen
dc.publisherHindawi Publishing Corpen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderCopyright © 2014 Mingming Liu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleA Transcriptome Post-Scaffolding Method for Assembling High Quality Contigsen
dc.title.serialComputational Biology Journalen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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