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bin/abacas.pl  view on Meta::CPAN

	-p	MUMmer program to use: 'nucmer' or 'promer'
OR
abacas.pl -r <reference file: single fasta>  -q <pseudomolecule/ordered sequence file: fasta> -e 
OPTIONS
        -h              print usage
	-d		use default nucmer/promer parameters 
	-s	int	minimum length of exact matching word (nucmer default = 12, promer default = 4)
	-m		print ordered contigs to file in multifasta format 
	-b		print contigs in bin to file 
	-N		print a pseudomolecule without "N"s 
	-i 	int 	mimimum percent identity [default 40]
	-v	int	mimimum contig coverage [default 40]
	-V	int	minimum contig coverage difference [default 1]
	-l	int	minimum contig length [default 1]
	-t		run tblastx on contigs that are not mapped 
	-g 	string (file name)	print uncovered regions (gaps) on reference to file name
	-n	int	insert n Ns between overlapping contigs [default 100]
	-a		append contigs in bin to the pseudomolecule
	-o	prefix  output files will have this prefix
	-P		pick primer sets to close gaps
	-f	int	number of flanking bases on either side of a gap for primer design (default 350)