title: TransRate: reference-free quality assessment of de novo transcriptome 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 samples.
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors.forename: Richard
authors.initials: R
authors.lastname: Smith-Unna
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors.forename: Chris
authors.initials: C
authors.lastname: Boursnell
authors.affiliation: Department of Computer Science, Stony Brook University, Stony Brook, New York 11794-4400, USA;
authors.forename: Rob
authors.initials: R
authors.lastname: Patro
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors.forename: Julian M
authors.initials: JM
authors.lastname: Hibberd
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom.
authors.forename: Steven
authors.initials: S
authors.lastname: Kelly
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D062085:RNA, Long Noncoding / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012984:Software; D059467:Transcriptome / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012335:RNA, Ribosomal