Fig. 1

ITD Assembler workflow schema. The major ITD Assembler processing steps are depicted with transitional blue arrows decreasing in size, representing a serial reduction in the number of reads at each step. To the left of the ITD Assembler workflow is an example read set containing two repeated kmers, one 6 bases and another 7 bases apart, which are placed into bins 6 and 7. De Bruijn graph construction is performed on these three example reads using, for illustration purposes, kmer length 3. The integer values near each vertex are the coverage of each vertex in the graph. There are two cycles of length 6 and 7 in this graph representing the two independent ITDs. OLC assembly is performed on those read sets from bins 6 and 7, with resulting contigs being annotated and ITDs reported