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TransRate: reference free quality assessment of de-novo transcriptome assemblies

View ORCID ProfileRichard Smith-Unna, View ORCID ProfileChris Boursnell, View ORCID ProfileRob Patro, View ORCID ProfileJulian M Hibberd, View ORCID ProfileSteven Kelly
doi: https://doi.org/10.1101/021626
Richard Smith-Unna
1Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, UK
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Chris Boursnell
1Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, UK
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Rob Patro
2Department of Computer Science, Stony Brook University, Stony Brook, NY 11794-4400, USA
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Julian M Hibberd
1Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, UK
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Steven Kelly
3Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, UK
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  • For correspondence: steven.kelly@plants.ox.ac.uk
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Abstract

TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only sequenced reads as the input, TransRate measures the quality of individual contigs and whole assemblies, enabling assembly optimization and comparison. TransRate can accurately evaluate assemblies of conserved and novel RNA molecules of any kind in any species. We show that it is more accurate than comparable methods and demonstrate its use on a variety of data.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 27, 2015.
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TransRate: reference free quality assessment of de-novo transcriptome assemblies
Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly
bioRxiv 021626; doi: https://doi.org/10.1101/021626
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TransRate: reference free quality assessment of de-novo transcriptome assemblies
Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly
bioRxiv 021626; doi: https://doi.org/10.1101/021626

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