NAME
HPC.damapper: - long read to reference genome mapping toolDESCRIPTION
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 mapsSYNOPSIS
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>
| August 2020 | damapper |