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

# repair(1)

toolkit for processing next-gen sequencing data

## NAME

repair - toolkit for processing next-gen sequencing data

## DESCRIPTION

repair Version 2.0.4

-

  Find reads that are from the same pair in the input and then place them next

to each other in the output. A dummy read is added for each singleton read that does not have a pair. The output file is compatible with featureCounts program.

Usage:

-

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

Required arguments:

- **-i** \<string\>

  Name of input file. BAM format by default.

- **-o** \<string\>

  Name of output file. The output file is in BAM format.

Optional arguments:

- **-S**

  The input file is in SAM format.

- **-c**

  Compress the output BAM file. This will reduce the size of BAM file, but will increase the time of retrieving reads from BAM file.

- **-T** \<int\>

  Number of CPU threads. 8 by default.

- **-d**

  Do not add dummy reads for singleton reads.

- **-t**

  Do not include sequences and quality scores of reads in the output file.

## AUTHOR

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