HPC.damapper1
Long read to reference genome mapping tool
Usage
HPC.damapper [-vpzCN]
[-k<int(20)>]
[-t<int>]
[-M<int>]
[-e<double(.85)]
[-s<int(100)]
Overview
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>.
Overview
[-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>
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).