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Structural variations are a complex collection of mutations, many of which are reported to associated to complex traits. Recent research reports a rare case of structural variants, complex indels, which may contribute to carcinogenesis. A complex indel often presents multiple inserted nucleotides in a deleted region. Due to the limitations on both data and algorithm, existing approaches could only detect complex indels with the length shorter than 80bps; however, the longer ones are considered to imply stronger impact. In this paper, we propose a novel algorithm, SVseq3, which handles the PacBio data and identifies the long complex indels. The algorithm captures the BLASR alignment results and locates the suspicious areas of complex indels by clustering. An improved similarity hash-based framework is then constructed. For each suspicious area, a continuing-seed strategy is adopted to split the inserted …