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LR_Gapcloser is an efficient and fast tool using long reads to close gaps. Tested among various assemblies of short contigs with long reads, LR_Gapcloser closed almost all gaps with high accuracy over 99.3%. The contig N50 sizes had 15~251 fold increases. Compared with other tools of a sort, this tool closed the most gaps and had the fastest speed. It was 2~239 fold faster than other tools. We also studied the effect of sequencing coverages to the gap-closure performance and accuracy.