pip install hicshuffle

Commands:
    diff            FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis
Run hicshuffle <command> -h for help on a specific command.

HiCShuffle: FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis

positional arguments:
  command     Subcommand to run

optional arguments:
  -h, --help  show this help message and exit
  --version   show program's version number and exit

FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis

positional arguments:
  query_path_1      Path for READ1 of GZ-Compressed or Uncompressed Query FASTQ
  query_path_2      Path for READ2 of GZ-Compressed or Uncompressed Query FASTQ
  reference_path_1  Path for READ1 of GZ-Compressed or Uncompressed Reference FASTQ
  reference_path_2  Path for READ2 of GZ-Compressed or Uncompressed Reference FASTQ
  output_directory  Output Directory... HiCShuffle Will Generate Output Directory If Not Existent

optional arguments:
  -h, --help         show this help message and exit