Two-Pass Splice Junction Alignment

Instead of using a GTF file for annotated splice junctions, the DRAGEN software is also capable of reading in an SJ.out.tab file (see SJ.out.tab). This file enables DRAGEN to run in a two-pass mode, where the splice junctions discovered in the first pass (output as SJ.out.tab file) are used to guide the mapping and alignment reads during a second run through DRAGEN. This mode of operation is useful to increase sensitivity for spliced alignments in cases when a gene annotations file is not readily available for the target genome.