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AugmentingAssembly
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modified on 2015-12-14, 05:41 Researchers interested in studying and constructing transcriptomes,
especially for non-model species, face the conundrum of choosing from a
number of available de novo and genome-guided assemblers. None of
the popular assembly tools in use today achieve requisite sensitivity,
specificity or recovery of full-length transcripts on their own. Here,
we present a comprehensive comparative study of the performance of
various assemblers. Additionally, we present an approach to
combinatorially augment transciptome assembly by using both de novo
and genome-guided tools. In our study, we obtained the best recovery
and most full-length transcripts with Trinity and TopHat1-Cufflinks,
respectively. The sensitivity of the assembly and isoform recovery was
superior, without compromising much on the specificity, when transcripts
from Trinity were augmented with those from TopHat1-Cufflinks.