# HiCShuffle
[](https://badge.fury.io/py/HiCShuffle)
[](https://doi.org/10.1101/2021.09.23.459925)
[](https://lbesson.mit-license.org/)
**FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis**
## Installation
```shell
pip install hicshuffle
```
## Usage
### hicshuffle <command> [options]
```shell
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
```
### hicshuffle diff [-h] query_path_1 query_path_2 reference_path_1 reference_path_2 output_directory
```shell
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
```
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