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dc.creatorGhaffari, Noushin
dc.creatorArshad, Osama A.
dc.creatorJeong, Hyundoo
dc.creatorThiltges, John
dc.creatorCriscitiello, Michael F.
dc.creatorYoon, Byung-Jun
dc.creatorDatta, Aniruddha
dc.creatorJohnson, Charles D.
dc.date.accessioned2015-06-05T21:05:07Z
dc.date.available2015-06-05T21:05:07Z
dc.date.issued2015-06-05
dc.identifier.urihttps://hdl.handle.net/1969.1/154308
dc.description.abstractNew de novo transcriptome assembly and annotation methods provide an incredible opportunity to study the transcriptome of organisms that lack an assembled and annotated genome. There are currently a number of de novo transcriptome assembly methods, but it has been difficult to evaluate the quality of these assemblies. In order to assess the quality of the transcriptome assemblies, we composed a workflow of multiple quality check measurements that in combination provide a clear evaluation of the assembly performance. We presented novel transcriptome assemblies and functional annotations for Pacific whiteleg shrimp (Litopenaeus vannamei), a mariculture species with great national and international interest, and no solid transcriptome/genome reference. We examined Pacific whiteleg transcriptome assemblies via multiple metrics, and provide an improved gene annotation. Our investigations show that assessing the quality of an assembly purely based on the assembler’s statistical measurements can be misleading; we propose a hybrid approach that consists of statistical quality checks and further biological-based evaluations.en
dc.language.isoen_US
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectbioinformaticsen
dc.subjectPacific whiteleg shrimpen
dc.subjectLitopenaeus vannameien
dc.subjecttranscriptome assemblyen
dc.subjectworkflow evaluationen
dc.titleExamining De Novo Transcriptome Assemblies via a Quality Assessment Pipelineen
dc.typePreprinten
local.departmentOtheren


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Attribution-NonCommercial-NoDerivatives 4.0 International
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 International