---
name: "HPC.damapper"
section: "1"
platform: "linux"
package: "damapper"
version: "0.0+git20240314.b025cf9-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/HPC.damapper"
---

# HPC.damapper(1)

long read to reference genome mapping tool

## 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\>