Fig. 13

The entire workflow of TraRECo assembly procedure consisting of (1) contig growing, (2) junction search and splice graph construction and (3) joint isoform detection and abundance estimation. In contig growing step, we employed greedy approach and consensus-matrix based error-aware alignment test. In junction search, we test alignment of prefix and suffix of a contig with other contigs. The aligned prefix and suffix contain chimeric reads that span over two consecutive exon, even though they might have been aligned because of sequence repeat. The inner end of aligned prefix or suffix will possibly be the junction boundary between two consecutive exons. In joint isoform detection and abundance estimation, we used a modified version of IsoLasso, by which one can remove the transcript candidates according to their estimated abundance