Fig. 1

Example of a splice graph by representing long reads as phasing paths and its decomposition with and without preservation of long reads’ phasing paths. a Alignment of reads to the reference genome. Inferred (partial) exons are marked with letters. Green and blue colored reads are long reads spanning more than two exons. Scallop-LR represents these long reads as a set of phasing paths: {(a,c,e),(b,c,d)}. b The corresponding splice graph (with weights for all edges) and associated phasing paths (in green and blue). c Decomposition of the splice graph without preservation of long reads’ phasing paths. Although all weights are perfectly matched, both phasing paths are “broken” (none of the three decomposed paths contains (b,c,d) or (a,c,e)). d Decomposition of the splice graph with preservation of long reads’ phasing paths. All phasing paths are correctly covered by assembled transcripts