ParaPindel A Parallel Detection Framework for Structural Variation

ParaPindel, an optimized version of serial Pindel that utilizes distributed multi-process and shared multi-threading, for efficient large-scale detection of structural variation for human whole-genome sequencing data. ParaPindel divides the chromosome into multiple small windows with a fixed-length window size, so as to realize the parallel detection between different windows and different chromosomes. A cross-window with a smaller length is introduced to cope with possible structural variations at the edge of the window. The experimental results show that ParaPindel shortens the time to detect an individual's genome-wide structural variation from 186 hours to 33 minutes under the premise that the detection results are basically consistent. Employing 256 processes on 128 nodes on the TH-1HN supercomputer, the speedup ratio has reached 163 times, and the parallel efficiency has reached 69.74%.