| Name | Chimera-Buster JSON |
| Version |
1.2.1
JSON |
| download |
| home_page | https://github.com/JessicaA2019/Chimera_Buster |
| 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 |
| upload_time | 2024-06-21 21:49:29 |
| maintainer | None |
| docs_url | None |
| author | Jessica Lauren ALbert |
| requires_python | >=3 |
| 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. |
| keywords |
hiv
umis
pcr
chimeras
ont sequencing
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Chimera_Buster
### Overview
This package takes concensus fasta files from the MrHamer2.0 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
##### Requires python<=3.10
## Quick Install
```bash
pip install Chimera_Buster
```
## Manual Install
```bash
git clone https://github.com/JessicaA2019/Chimera_Buster.git
cd Chimera_Buster
python setup.py install
```
## Dependencies
Some dependencies currently do not install with Chimera_Buster. Please pip install the following dependencies:
* edlib
* pandas
* multiprocessing
* argparse
******************
## Usage
Chimera_Buster [options] {input_file_name} {input_prelim_name} {output_file_prefix}
### Inputs
To run the pipeline the following input files are required:
| Input | Description |
| ------ | ------ |
|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.|
The following input files are optional:
| Arguement | Function |
| ------ | ------ |
|-h, --help | Prints help message to terminal. |
|-m int, --mismatch int| Designates the maximum number of mismatched/indel bases allowed when comparing UMIs. Default is 1. |
|-c True/False, --check_clusters True/False | When set to true, chimeric reads are rechecked to account for any clustering issues earlier in the pipeline. WARNING: this part of the code is slow and is only recommended for low input samples. Default is False. |
### Outputs
The main output files created by the pipeline are:
| Output | Description |
|--------|-------------|
| {output_file_prefix}_chimera_list.txt | A list of all chimeric sample IDs. |
| {output_file_prefix}_nonchimera_list.txt | A list of all nonchimeric sample IDs. |
| {output_file_prefix}_chimeras.csv | A csv of the sample ID, UMI sequences, and cluster counts for each chimeric read. |
| {output_file_prefix}_non_chimeras.csv | A csv of the sample ID, UMI sequences, and cluster counts for each nonchimeric read. |
**************************
## Help
For issues or bugs, please report them on the [issues page][issues].
## License
MIT - Copyright (c) 2024 Jessica Lauren Albert
[//]: # (These are reference links used in the body of this note and get stripped out when the markdown processor does its job. There is no need to format nicely because it shouldn't be seen. Thanks SO - http://stackoverflow.com/questions/4823468/store-comments-in-markdown-syntax)
[issues]: <https://github.com/JessicaA2019/Chimera_Buster/issues>
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"description": "# Chimera_Buster\n### Overview\nThis package takes concensus fasta files from the MrHamer2.0 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.\n******************\n## Installation\n##### Requires python<=3.10\n## Quick Install\n```bash\npip install Chimera_Buster\n```\n## Manual Install\n```bash\ngit clone https://github.com/JessicaA2019/Chimera_Buster.git \ncd Chimera_Buster\npython setup.py install\n```\n## Dependencies\nSome dependencies currently do not install with Chimera_Buster. Please pip install the following dependencies:\n* edlib\n* pandas\n* multiprocessing\n* argparse\n\n******************\n## Usage\n Chimera_Buster [options] {input_file_name} {input_prelim_name} {output_file_prefix}\n### Inputs\nTo run the pipeline the following input files are required:\n| Input | Description |\n| ------ | ------ |\n|input_file_name | Designates clusters_concesus.fasta file from the clustering_consensus folder to be filtered. This is required.|\n| input_prelim_name | Designates clusters_concesus.fasta file from the clustering folder to be filtered. This is required.|\n| output_file_prefix | Designates output file prefix. This is required.|\nThe following input files are optional:\n| Arguement | Function |\n| ------ | ------ |\n|-h, --help | Prints help message to terminal. |\n|-m int, --mismatch int| Designates the maximum number of mismatched/indel bases allowed when comparing UMIs. Default is 1. |\n|-c True/False, --check_clusters True/False | When set to true, chimeric reads are rechecked to account for any clustering issues earlier in the pipeline. WARNING: this part of the code is slow and is only recommended for low input samples. Default is False. |\n\n### Outputs\n The main output files created by the pipeline are:\n| Output | Description |\n|--------|-------------|\n| {output_file_prefix}_chimera_list.txt | A list of all chimeric sample IDs. |\n| {output_file_prefix}_nonchimera_list.txt | A list of all nonchimeric sample IDs. |\n| {output_file_prefix}_chimeras.csv | A csv of the sample ID, UMI sequences, and cluster counts for each chimeric read. |\n| {output_file_prefix}_non_chimeras.csv | A csv of the sample ID, UMI sequences, and cluster counts for each nonchimeric read. |\n\n**************************\n## Help\nFor issues or bugs, please report them on the [issues page][issues]. \n\n## License\n\nMIT - Copyright (c) 2024 Jessica Lauren Albert\n\n[//]: # (These are reference links used in the body of this note and get stripped out when the markdown processor does its job. There is no need to format nicely because it shouldn't be seen. Thanks SO - http://stackoverflow.com/questions/4823468/store-comments-in-markdown-syntax)\n\n [issues]: <https://github.com/JessicaA2019/Chimera_Buster/issues>\n",
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