Metadata-Version: 2.1
Name: Chimera_Buster
Version: 1.1.0
Summary: eliminates chimeric reads by comparing the UMI sequences and finding any matches in the 5 prime or 3 prime UMIs and keeping the sequence that has the highest prevalence
Home-page: https://github.com/JessicaA2019/Chimera_Buster
Author: Jessica Lauren ALbert
Author-email: Jessica Lauren Albert <jessica.albert2001@gmail.com>
License: MIT License
        
        Copyright (c) 2024 Jessica Lauren Albert
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/JessicaA2019/Chimera_Buster
Keywords: HIV,UMIs,PCR,chimeras,ONT sequencing
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3
Description-Content-Type: text/markdown
License-File: LICENSE.txt

# Chimera_Buster


This package takes concensus fasta files from the MrHamer pipeline and eliminates chimeric reads by comparing the UMI sequences and finding any matches in the 5' or 3' UMIs and keeping the sequence that has the highest prevalence.

## Installation



## Usage
    python3 CLI_chimera_buster_pd.py [options] input_final_name input_prelim_name output_file_prefix

positional arguments:
| Arguement | Function |
| ------ | ------ |
|input_file_name  |    Designates clusters_concesus.fasta file from the clustering_consensus folder to be filtered. This is required.|
|  input_prelim_name     |    Designates clusters_concesus.fasta file from the clustering folder to be filtered. This is required..|
|  output_file_prefix  |  Designates output file prefix. This is required.|

options:
| Arguement | Function |
| ------ | ------ |
|-h, --help |  show this help message and exit |
|-m int, --mismatch int|  Designates the maximum number of mismatched/indel bases allowed. Default is 1. |

## License

MIT - Copyright (c) 2024 Jessica Lauren Albert

