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Pacbio_Gapcloser is an efficient and fast tool using long reads to close gaps. Tested among various organisms with long reads, Pacbio_Gapcloser closed almost all gaps with high accuracy over 99.5%. The contig N50 sizes had 15~251 fold increases. Compared to other tools of a sort, this tool closed the most gaps and had the highest accuracy. It was 2~1,000 fold faster than other tools. We also studied the effect of sequencing depth of long reads to the gap-closure performance and accuracy.