A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads

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dc.contributor.authorMbandi, Stanley K.
dc.contributor.authorHesse, Uljana
dc.contributor.authorRees, Jasper G.
dc.contributor.authorChristoffels, Alan
dc.date.accessioned2015-06-09T14:47:07Z
dc.date.available2015-06-09T14:47:07Z
dc.date.issued2014
dc.description.abstractDownstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using a quality score. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly. Using RNA-Seq data produced from Illumina,we teased out the effects of quality score based filtering or trimming on de novo transcriptome reconstruction. We showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. Our data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, our results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enables election of the optimum de novo transcriptome assembly in non-model organisms.en_US
dc.description.sponsorshipSouth African Research Chair Initiative National Research Foundation of South Africaen_US
dc.identifier.citationMbandi, S.K. et al. (2014). A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads. Frontiers in Genetics, 5(17): 1-5en_US
dc.identifier.issn1664-8021
dc.identifier.urihttp://hdl.handle.net/10566/1503
dc.language.isoenen_US
dc.privacy.showsubmitterfalse
dc.publisherFrontiers
dc.rights© 2014 Mbandi, Hesse, Rees and Christoffels. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/
dc.source.urihttp://dx.doi.org/10.3389/fgene.2014.00017
dc.status.ispeerreviewedtrue
dc.subjectRNA-Seqen_US
dc.subjectQuality scoreen_US
dc.subjectTrinityen_US
dc.subjectTranscriptome reconstructionen_US
dc.subjectTruncated transfragsen_US
dc.subjectOasesen_US
dc.titleA glance at quality score: implication for de novo transcriptome reconstruction of Illumina readsen_US
dc.typeArticleen_US

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