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DRAP: de novo RNA-Seq Assembly Pipeline

Abstract : Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set.
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https://hal.inrae.fr/hal-02789567
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Submitted on : Friday, June 5, 2020 - 5:20:47 AM
Last modification on : Wednesday, November 3, 2021 - 7:25:36 AM

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Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, et al.. DRAP: de novo RNA-Seq Assembly Pipeline. 2017. ⟨hal-02789567⟩

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