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11 TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. 12 Using only sequenced reads as the input, TransRate measures the quality of individual contigs 13 and whole assemblies, enabling assembly optimization and comparison. TransRate can 14 accurately evaluate assemblies of conserved and novel RNA molecules of any kind in any 15 species. We show that it is more accurate than comparable methods and demonstrate its use 16 on a variety of data. 17 Introduction 18 High-throughput sequencing of RNA has revolutionized our ability to assess the genetic basis of 19 biological traits. For organisms that have sequenced and annotated genomes gene expression, splice20 variants and mutations can be estimated from alignment of reads direct to the genome. In the absence 21 of an appropriate reference genome, de novo transcriptome assembly is required. 22 Many de-novo assembly algorithms have been developed, including Trinity (Grabherr et al., 2011), 23 Oases (Schulz et al., 2012), and SOAPdenovo-Trans (Xie et al., 2014), each of which takes a different 24 approach to the problem. These tools provide multiple parameters and heuristics that can be modified 25 . CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/021626 doi: bioRxiv preprint first posted online Jun. 27, 2015;