EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds.
EndHiC takes the HiC-pro's bin matrix results as input data. After running HiC-pro, the recommended EndHiC usage for most users is to run endhic.pl or endhic_auto.pl. When your contig assembly is quite good, then endhic.pl [one round of EndHiC] is able to finish the job; When your contig assembly is relatively fragmental, then endhic_auto.pl [multiple rounds of EndHiC] should be used. How many rounds is needed depend on the contig assembly level, and more fragmental contigs need higher rounds of EndHiC.
module add endhic-1.0.0