TransRate: reference-free quality assessment of de novo transcriptome assemblies
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TLDR
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies using only the sequenced reads and the assembly as input and it is revealed that variance in the quality of the input data explains 43% of the variance inThe quality of published de noVO transcriptome assembly assemblies.Abstract:
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected These include chimeras, structural errors, incomplete assembly, and base errors TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samplesread more
Citations
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Using SPAdes De Novo Assembler
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References
More filters
Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Journal ArticleDOI
BLAST+: architecture and applications.
Christiam Camacho,George Coulouris,Vahram Avagyan,Ning Ma,Jason S. Papadopoulos,Kevin Bealer,Thomas L. Madden +6 more
TL;DR: The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences.
Journal ArticleDOI
QUAST: quality assessment tool for genome assemblies
TL;DR: This tool improves on leading assembly comparison software with new ideas and quality metrics, and can evaluate assemblies both with a reference genome, as well as without a reference.
Journal ArticleDOI
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
Marcel H. Schulz,Marcel H. Schulz,Marcel H. Schulz,Daniel R. Zerbino,Daniel R. Zerbino,Martin Vingron,Ewan Birney +6 more
TL;DR: A software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms is presented.
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