Fig. 1

a A gene in the genome (top) and its corresponding transcripts (middle) compared to the superTranscript for the same gene (bottom). Colours indicate superTranscript blocks. b A schematic diagram showing the steps in Lace’s algorithm. A superTranscript (at the bottom) is built from transcripts A and B (blue and red, respectively). For each transcript, Lace builds a directed graph with a node for each base. Transcripts are aligned against one another using blat and the nodes of shared bases are merged. Lace then simplifies the graph by compacting unforked edges. The graph is topologically sorted and the resulting superTranscript annotated with transcripts and blocks. c The general workflow we propose for RNA-seq analysis in non-model organisms. Reads are de novo assembled, transcripts clustered into genes, superTranscripts assembled using Lace and reads aligned back. Here we use Trinity, Corset and STAR as our assembler, clustering program and aligner, respectively, but equivalent tools could also be used