├── HiC-ImpScaffolding ├── OM.find.conflict-regions.for.HiC.improved.pl ├── OM.scaffolding.pl ├── OM.split-misassembly.pl ├── README.md ├── hirise_commands.pa.sh └── run.sh ├── LICENSE ├── OM-ImpScaffolding ├── OM.falcon.pbcr.misass.cross-check.pl ├── OM.find.conflict-regions.pl ├── OM.merge.conflict-regions.pl ├── OM.scaffolding.pl ├── OM.split-misassembly.pl ├── README.md └── run.sh ├── PacBio ├── fc_run.cfg └── pbcr.pacbio.spec ├── README.md ├── data └── readme.txt ├── hybridScaffold.pl ├── integrated-OM-HiC-scaffolding ├── OM.breaks.ctg.pl ├── OM.breaks.filter.pl ├── OM.conflicts.add.HiRise.pl ├── OM.conflicts.falcon-pbcr.cross-check.pl ├── OM.find.conflict-regions.pl ├── OM.merge.low-high.breaks.pl ├── OM.scaffolding.pl ├── OM.split-misassembly.pl ├── hirise_commands.pa.sh ├── readme.txt └── run.sh ├── scripts ├── AssignAlignType.pl ├── MergeNGS_BN.pl ├── calc_cmap_stats.pl ├── calc_xmap_stats.pl ├── fa2cmap.pl ├── fa_key_convert.pl ├── findBNG.pl ├── findNGS.pl ├── per5 │ └── 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