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The underlying algorithm consists of three key steps in the procedure:
1) Searching virus genomes for soft-clip reads to detect virus putative break points (Fig. 1 steps 1-2).
2) Searching human-virus chimeric reads and merge adjacent or overlapping chimeric reads (with an insert-size extension on both side of read) to generate human genome blocks (Fig. 2).
3) The human genome blocks will be used as the mapping reference genome to identify virus integration sites, which largely reduce the alignment searching space and using De novo assembly and realign methods greatly raise the true positive rate. (Fig.1 steps 3-5)

Figure 1: VirusFaster Breakpoint Detection Procedure

Figure 2: Generation of Human Genome Blocks

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