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.