HPC.damapper(1)
long read to reference genome mapping tool
Description
HPC.DAMAPPER
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.
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-k: k-mer size (must be <= 32). |
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-t: Ignore k-mers that occur >= -t times in a block. |
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-M: Use only -M GB of memory by ignoring most frequent k-mers. |
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-e: Look for alignments with -e percent similarity. |
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-s: Use -s as the trace point spacing for encoding alignments. |
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-n: Output all matches within this % of the best |
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-T: Use -T threads. |
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-P: Do sorts and merges in directory -P. |
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-m: Soft mask the blocks with the specified mask. |
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-b: For AT/GC biased data, compensate k-mer counts (deprecated). |
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-z: sort .las by A,B-read pairs (overlap piles) |
off => sort .las by A-read,A-position pairs (default for mapping)
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-p: Output repeat profile track |
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-C: Output reference vs reads .las. |
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-N: Do not output reads vs reference .las. |
Script control.
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-v: Verbose mode, output statistics as proceed. |
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-B: # of block compares per daligner job |
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-f: Place script bundles in separate files with prefix <name> |