Figure 1

Overview of the split-read strategy. Each read is split into two pieces, or "anchors," of equal length (red and blue), with a gap between them. The anchors are aligned independently, and only the instances in which both align uniquely to the reference sequence are considered. Then, the alignments are extended as long as they still match the reference sequence. The SplitSeek program identifies all candidate junction reads from the split-read alignments where the boundary is located in the gap between the anchors. Then additional junction reads are detected from the set of reads that partly align to a previously detected candidate junction, and where the remaining, nonaligned, part of the read (grey lines) has a 5-bp identical sequence compared with the corresponding part of the same candidate read. SplitSeek then groups all potential junction reads, applies cut-offs, and reports the results.