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Manual

DAMAPPER

NAME
DESCRIPTION
SYNOPSIS

NAME

damapper - long read to reference genome mapping tool

DESCRIPTION

Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool.

SYNOPSIS

damapper [ -vpzCN ] [ -k<int(20)> ] [ -t<int> ] [ -M<int> ] [ -T<int(4)> ] [ -P<dir(/tmp)> ] [-e<double(.85)] [-s<int(100)>] [-n<double(1.00)>] [-m<track>]+ <reference:dam> <reads:db> ...

	-k : k-mer size (must be <= 32).
	-t : Ignore k-mers that occur >= -t times in a block.
	-M : Use only -M GB of memory by ignoring most frequent k-mers.
	-e : Look for alignments with -e percent similarity.
	-s : Use -s as the trace point spacing for encoding alignments.
	-n : Output all matches within this % of the best
	-T : Use -T threads.
	-P : Do sorts and merges in directory -P .
	-m : Soft mask the blocks with the specified mask.
	-v : Verbose mode, output statistics as proceed.
	-z : sort .las by A,B-read pairs (overlap piles)

off => sort .las by A-read,A-position pairs (default for mapping)

	-p : Output repeat profile track
	-C : Output reference vs reads .las.
	-N : Do not output reads vs reference .las.