Fig. 4
From: Correction to: SLR: a scaffolding algorithm based on long reads and contig classification
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