NAME

HPC.damapper: - long read to reference genome mapping tool

DESCRIPTION

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

Compared to damapper, this writes a UNIX shell script to the standard output that maps
every read in blocks <first> to <last> of database <reads> to a reference sequence <ref>.

SYNOPSIS

HPC.damapper [-vpzCN] [-k<int(20)>] [-t<int>] [-M<int>] [-e<double(.85)] [-s<int(100)]

DESCRIPTION

[-n<double(1.)] [-m<track>]+ [-B<int( 4)>] [-T<int(4)>] [-f<name>]

<ref:db|dam> <reads:db|dam> [<first:int>[-<last:int>]]

Passed through to damapper.

-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.

-b: For AT/GC biased data, compensate k-mer counts (deprecated).

-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.

Script control.

-v: Verbose mode, output statistics as proceed.

-B: # of block compares per daligner job

-f: Place script bundles in separate files with prefix <name>