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lrgapcloser website  

LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.

Environment Modules

Run module spider lrgapcloser to find out what environment modules are available for this application.

System Variables

  • HPC_LRGAPCLOSER_DIR - installation directory
  • HPC_LRGAPCLOSER_BIN - executable directory