Fig. 3

De novo supertranscriptome assembly error signatures used by ROAST to identify various types of assembly errors. a Incompleteness of the supertranscripts is detected using unmapped or partially reads (reads containing soft-clipped bases) at the edges of the contig. b Fragmented contigs are identified using partially mapped reads such that the soft-clipped bases map on different contigs and using reads with mates mapped on different contigs. c False chimeras are identified using partially mapped reads occurring inside a contig as well as based on unusual change in expression level along a contig. d Local mis-assemblies can be detected using partially mapped reads with soft-clipped bases occurring in either a crisscross fashion (missing sequences, inversions and translocations) or facing towards each other (unsupported insertions)