Cooltools: enabling high-resolution Hi-C analysis in Python
Cooltools is a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface and Python application programming interface, which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments.
References:
- Open2C, Nezar Abdennur, Sameer Abraham, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A.
Galitsyna, Anton Goloborodko, Maxim Imakaev, Betul A. Oksuz, Sergey V. Venev,
Cooltools: enabling high-resolution Hi-C analysis in Python
Nature Communications 12, Article number: 3836 (2021).
Documentation
Important Notes
- Module Name: cooltools (see the modules page for more information)
- Unusual environment variables set
- CT_HOME installation directory
- CT_BIN executable directory
- CT_DATA sample data directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cig 3335 ~]$ module load cooltools [+] Loading singularity 3.10.5 on cn3335 [+] Loading cooltools 0.5.4 [user@cn3335 ~]$ cooltools Usage: cooltools [OPTIONS] COMMAND [ARGS]... Type -h or --help after any subcommand for more information. Options: -v, --verbose Verbose logging -d, --debug Post mortem debugging -V, --version Show the version and exit. -h, --help Show this message and exit. Commands: coverage Calculate the sums of cis and genome-wide contacts (aka... dots Call dots on a Hi-C heatmap that are not larger than... eigs-cis Perform eigen value decomposition on a cooler matrix to... eigs-trans Perform eigen value decomposition on a cooler matrix to... expected-cis Calculate expected Hi-C signal for cis regions of... expected-trans Calculate expected Hi-C signal for trans regions of... genome Utilities for binned genome assemblies. insulation Calculate the diamond insulation scores and call... pileup Perform retrieval of the snippets from .cool file. random-sample Pick a random sample of contacts from a Hi-C map. saddle Calculate saddle statistics and generate saddle plots... virtual4c Generate virtual 4C profile from a contact map by... [user@cn3335 ~]$ ct_python Python 3.8.18 (default, Sep 11 2023, 13:40:15) [GCC 11.2.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. >>> import cooltools >>>