Transcriptome assembly statistics for Agalma elegans . (a) Cumulative read coverage, sorted from the most frequently sequenced exemplar transcripts to the least frequently sequenced transcripts. Most reads map to a small fraction of the genes, as is typical for a transcriptome sequencing project. (b) The size distribution of the assembled transcripts, for all transcripts and for only those transcripts that have a blastx hit to a protein in the Swissprot database. Most small transcripts do not have blastx hits and likely include some non-coding RNA and many assembly errors. These are removed prior to phylogenetic analysis. See Additional file 1 for further assembly diagnostics.