---
name: "cooler"
section: "1"
platform: "linux"
package: "python3-cooler"
version: "0.10.3-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cooler"
---

# cooler(1)

sparse, compressed, binary persistent storage

## NAME

cooler - sparse, compressed, binary persistent storage

## SYNOPSIS

**cooler** \[*OPTIONS*\] *COMMAND* \[*ARGS*\]...

## DESCRIPTION

Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.

The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files.

## OPTIONS

- **-v**, **--verbose**

  Verbose logging.

- **-d**, **--debug**

  On error, drop into the post-mortem debugger shell.

- **-V**, **--version**

  Show the version and exit.

- **-h**, **--help**

  Show this message and exit.

### Commands:

- cload

  Create a cooler from genomic pairs and bins.

- load

  Create a cooler from a pre-binned matrix.

- merge

  Merge multiple coolers with identical axes.

- coarsen

  Coarsen a cooler to a lower resolution.

- zoomify

  Generate a multi-resolution cooler file by coarsening.

- balance

  Out-of-core matrix balancing.

- info

  Display a cooler's info and metadata.

- dump

  Dump a cooler's data to a text stream.

- show

  Display and browse a cooler in matplotlib.

- makebins

  Generate fixed-width genomic bins.

- digest

  Generate fragment-delimited genomic bins.

- csort

  Sort and index a contact list.

- ls

  List all coolers inside a file.

- cp

  Copy a cooler from one file to another or within the same file.

- ln

  Create a hard link to a cooler (rather than a true copy) in the...

- mv

  Rename a cooler within the same file.

- tree

  Display a file's data hierarchy.

- attrs

  Display a file's attribute hierarchy.

## AUTHOR

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