DESCRIPTION
        ZORRO is an hybrid sequencing technology assembler. It takes to sets of
        pre-assembled contigs and merge them into a more contiguous and consistent
        assembly.

AUTHORS
        Gustavo Gilson Lacerda Costa, glacerda@lge.ibi.unicamp.br
        Ramon Oliveira Vidal, vidal@lge.ibi.unicamp.br
        Marcelo Falsarella Carazzolle, mcarazzo@lge.ibi.unicamp.br


REQUIREMENTS
	-BioPerl 1.6
	-AMOS 2.0.8
	-MuMMer 3.06
	-Bowtie 0.12.5
Please ensure that the following binaries are in your PATH
	-nucmer
	-delta-filter
	-show-coords
	-bowtie-build
	-bowtie
	-toAmos
	-kmer-cov-plot
	-count-kmers
	-bank-transact
	-bank-mapping
	-nucmerAnnotate
	-nucmer2ovl
	-ovl2OVL	
	-tigger
	-make-consensus
	-bank2contig
	-bank2fasta
	-listReadPlacedStatus
	-dumpreads

Usage:
     Use:
     zorro.pl 
     [--overlap int] [--identity float] [--[no]verbose]]
     [--[no]assembly1break]] [--[no]assembly2break]]
     --assembly1 path --assembly2 path --prefix string 
     --readset path --kmersize int

     Examples:
     #Merges 2 assemblies
     zorro.pl
     --assembly1 454AllContigs.fna 
     --assembly2 contigs.fa 
     --readset 454reads.fasta

Options:
     Arguments:
     --assembly1     | -1  fastafile Path to fasta file containing assembly1 (Required)
     --assembly2     | -2  fastafile Path to fasta file containing assembly2 (Required)
     --readset       | -r  fastafile Path to fasta file containing readset (Required)
     --prefix        | -p  string    Filename prefix for output files (Default: out)
     --overlap       | -o  int       Minimum overlap to be detected (Default: 40).
     --identity      | -i  float     Minimum identity in the overlap region (Default: 94)
     --overhang      | -g  int       Maximum alignment overhang (Default: 15)
     --kmersize      | -k  int       K-mer size to use in the repeat masking module (Default: 22)
     --maskinglevelA | -a int        Manually sets masking level A (Default: AUTO)
     --maskinglevelB | -b int        Manually sets masking level B (Default: AUTO)
     --maxmerge      | -m int        Merges neighbouring masked regions within maxmerge bp (Default: 100)
     Switches:
     --[no]assembly1break | -x Enables/disables BRK phase for assembly1 contigs (Default: enabled)
     --[no]assembly2break | -y Enables/disables BRK phase for assembly2 contigs (Default: enabled)
     --[no]verbose        | -v  Enables/disables verbosity
     --help               | -h  Displays help message