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.
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 >>>