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

# damapper(1)

long read to reference genome mapping tool

## NAME

damapper - long read to reference genome mapping tool

## DESCRIPTION

Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool.

## SYNOPSIS

**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)

-

  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.