TY - JOUR T1 - Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes JF - bioRxiv DO - 10.1101/323576 SP - 323576 AU - Lisa K. Johnson AU - Harriet Alexander AU - C. Titus Brown Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/09/18/323576.abstract N2 - Background De novo transcriptome assemblies are required prior to analyzing RNAseq data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines”, on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short read data collected by the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP). The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research (NCGR).Results New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics, with assemblies from the Dinoflagellata and Ciliophora phyla showing a higher percentage of open reading frames and number of contigs than transcriptomes from other phyla.Conclusions Given current bioinformatics approaches, there is no single ‘best’ reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally-intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.Key PointsRe-assembly with new tools can yield new resultsAutomated and programmable pipelines can be used to process arbitrarily many samples.Analyzing many samples using a common pipeline identifies taxon-specific trends.List of abbreviationsBLASTBasic Local Alignment Search ToolCRBBConditional Recriprocal Best BLASTDIBData Intensive Biology Lab at the University of California DavisHLLHyperLogLogMMETSPMarine Microbial Eukaryotic Transcriptome Sequencing ProjectNCGRNational Center for Genome ResearchORFOpen Reading FrameNCBINational Center for Biotechnology InformationSRASequence Read Archive ER -