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
pip install Chimera_Buster
Manual Install
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.
License
MIT - Copyright (c) 2024 Jessica Lauren Albert
1 maintainer
Metadata
1 maintainer
Release files for Chimera-Buster 1.2.1
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Source distribution (sdist)
| File | Size | Uploaded | |
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| chimera_buster-1.2.1.tar.gz | 9.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| Chimera_Buster-1.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 17.1 kB
Release files / chimera_buster-1.2.1.tar.gz
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| Size | 9.0 kB |
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