Fig. 4.
An example of alignment position revision. For an alignment given by the alignment tool, the region [ sr11, er11] (region3) in the long read lr1 is aligned with the region [ sc11, ec11] (region1) in the contig c1. Because sr11<sc11 and LEN(lr1)−er11>LEN(c1)−ec11, it means the region [0, sr11] (region4) in lr1 is not aligned with c1, and the region [ ec11,LEN(c1)−1] (region2) is not aligned with lr1. However, when lr1 is truely aligned with c1 and the alignment is reliable, region4 should be aligned with the region [ sc11−sr11, sc11] in c1, and region2 should be aligned with the region [ er11, er11+LEN(c1)−ec11]. Because of the high sequencing error rate in long reads, the alignment tool usually does not provide accurate alignment start and end positions. Then, SLR sets sc11′=sc11−sr11, sr11′=0, ec11′=LEN(c1)−1 and er11′=er11+LEN(c1)−ec11. When the alignment is reliable, the region [ sc11′, ec11′] in c1 is aligned with the region [ sr11′, er11′] in lr1