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3D de novo assembly: version 180114

USAGE: ./run-asm-pipeline.sh [options] <path_to_input_fasta> <path_to_input_mnd> 

DESCRIPTION:
This is a script to assemble draft assemblies (represented in input by draft fasta and deduplicated list of alignments of Hi-C reads to this fasta as produced by the Juicer pipeline) into chromosome-length scaffolds. The script will produce an output fasta file, a Hi-C map of the final assembly, and a few supplementary annotation files to help review the result in Juicebox.

ARGUMENTS:
path_to_input_fasta			Specify file path to draft assembly fasta file.
path_to_input_mnd			Specify path to deduplicated list of alignments of Hi-C reads to the draft assembly fasta as produced by the Juicer pipeline: the merged_nodups file (mnd).

OPTIONS:
-m|--mode haploid/diploid			Runs in specific mode, either haploid or diploid (default is haploid).
-i|--input input_size			Specifies threshold input contig/scaffold size (default is 15000). Contigs/scaffolds smaller than input_size are going to be ignored.
-r|--rounds number_of_edit_rounds			Specifies number of iterative rounds for misjoin correction (default is 2).
-s|--stage stage					Fast forward to later assembly steps, can be polish, split, seal, merge and finalize.
-h|--help			Shows this help. Type --help for a full set of options.
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