##OM-HiC-scaffolding
Here the scripts are used in the paper "Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromatin conformation capture data". http://genome.cshlp.org/content/27/5/778
#Description These scripts are used to do genome assembly scaffolding in three ways:
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scaffolding using optical consensus maps and PacBio read assembly contigs from Falcon and PBcR
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scaffolding using Dovetail Hi-C reads and PacBio read assembly contigs from Falcon and PBcR
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scaffolding using optical consensus maps, Dovetail Hi-C reads and PacBio read assembly contigs from Falcon and PBcR
#System requirements
Perl(version >5.10); Bioperl
IrysSolve scripts http://www.bnxinstall.com/scripts/v3692/
RefAligner http://www.bnxinstall.com/RefalignerAssembler/Linux/SSE/
BLAST (makeblastdb, blastn)
HiRise (https://github.com/DovetailGenomics/HiRise_July2015_GR)
####requirements for HiRise
Python 3
BWA (version: 0.7.15-r1140)
samtools (version:1.2)
samblaster (https://github.com/GregoryFaust/samblaster)
Meraculous (http://downloads.sourceforge.net/project/meraculous20/release-2.0.5.tgz)
#Usage Please read the "README.md" and "run.sh" in each scaffolding worflow