| DAMAPPER(1) | User Commands | DAMAPPER(1) |
damapper - long read to reference genome mapping tool
Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool.
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)
-p: Output repeat profile track
-C: Output reference vs reads .las.
-N: Do not output reads vs reference .las.
| August 2020 | damapper |