LR_Gapcloser is an efficient and fast tool using uncorrected (Pacbio or Nanopore) 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 99.5%. The contig N50 sizes had 10~140 fold increases. Compared with other tools of a sort, this tool closed the most gaps and had the fastest speed with the lowest memory usage. It is much suitable for large genome.