TransRate: reference-free quality assessment of de novo transcriptome assemblies

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…

• BA
  Bill and Melinda Gates Foundation
• EC
  European Commission

  Award: 637765
• RB
  Royal Botanical Gardens, Kew
• DO
  Department of Biotechnology, Ministry of Science and Technology, India
• DF
  Department for International Development
• DF
  Directorate for Biological Sciences
• BA
  Biotechnology and Biological Sciences Research Council

  Award: BB/J011754/1