Fig. 2

Denoise joining-pairs by first making sure they are mapped to 5′-most and 3′-most gene models. a For each joining-pair connecting two contigs, AGOUTI assigns each end (i.e., forward and reverse) to 5′-most and 3′-most gene models on the two contigs. In this case, the ends of the joined contigs have been labeled 3′ and 5′, respectively. Doing so ensures that each joining-pair does not span any gene models (i.e., there are no intervening gene models). b A joining-pair fails to map to any gene model at the edges of the two contigs. AGOUTI does not use such joining-pairs in scaffolding. c The reverse end of the joining-pair is mapped to 5′ of the 5′-most gene model on Contig 2. AGOUTI will create an artificial gene model accordingly, and assign an end label of 5′. d Similarly to (C), the forward end is mapped to 3′ of the 3′-most gene model on Contig 1. AGOUTI will create an artificial gene model and assign an end label of 3′. e Orientation imposes an important constraint. In this case, joining the contigs in the correct orientation shows that there are multiple intervening gene models between them, and this pair is therefore ignored. Here we only show the gene models at the edges of the contigs. There can be many genes in between them