---
name: "removeDup"
section: "1"
platform: "linux"
package: "subread"
version: "2.0.8+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/removeDup"
---

# removeDup(1)

toolkit for processing next-gen sequencing data

## NAME

removeDup - toolkit for processing next-gen sequencing data

## DESCRIPTION

removeDup Version 2.0.4

-

  Remove duplicated reads.

### Usage:

-

  ./removeDup \[options\] **-i** \<input\_file\> **-o** \<output\_file\>

Required arguments:

**-i** \<string\> Name of input file in SAM/BAM format.

**-o** \<string\> Name of output SAM file including filtered reads. The format is

-

  BAM unless '-S' is specified.

Optional arguments:

- **-S**

  Generate the SAM format output.

- **-r** \<int\>

  Specify the duplication cutoff. All the reads mapped to a location are removed from the output if the number of reads mapped to this location is equal or higher than the cutoff. 10 by default.

**-t** \<string\> A directory storing temporary files generated by the program.

## AUTHOR

 This manpage was written by Alexandre Mestiashvili for the Debian distribution and\
  can be used for any other usage of the program.