2017
DOI: 10.1101/216994
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Leveraging multiple transcriptome assembly methods for improved gene structure annotation

Abstract: The performance of RNA-Seq aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Here we show that the accuracy of transcript reconstruction can be boosted by combining multiple methods, and we present a novel algorithm to integrate multiple RNA-Seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified metrics, while solving com… Show more

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Cited by 16 publications
(16 citation statements)
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References 40 publications
(52 reference statements)
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“…ORFs were predicted using TransDecoder 3.0.0 [ 10 ]. Scoring parameters for each species can be found in Mikado v1.0.1 [ 48 ], with a name scheme of species_name _scoring.yaml (e.g., “athaliana_scoring.yaml” for A. thaliana ). The same scoring files were used for all runs, both with simulated and real data.…”
Section: Methodsmentioning
confidence: 99%
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“…ORFs were predicted using TransDecoder 3.0.0 [ 10 ]. Scoring parameters for each species can be found in Mikado v1.0.1 [ 48 ], with a name scheme of species_name _scoring.yaml (e.g., “athaliana_scoring.yaml” for A. thaliana ). The same scoring files were used for all runs, both with simulated and real data.…”
Section: Methodsmentioning
confidence: 99%
“… Project name: Mikado Project home page: [ 1 ] Operating system(s): Linux Programming language: Python3 Other requirements: SnakeMake, BioPython, NumPY, SciPY, Scikit-learn, BLAST+ or DIAMOND, Prodigal or TransDecoder, Portcullis Available through: PyPI, bioconda, SciCruch (RRID: SCR_016159) License: GNU LGPL3 …”
Section: Availability Of Source Code and Requirementsmentioning
confidence: 99%
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