Metadata-Version: 2.4
Name: dropbucket
Version: 2.1.1
Summary: Robust SNP-based demultiplexing tool
Author-email: dongjuleem <ehdwn5170@g.skku.edu>
Maintainer-email: dongjuleem <ehdwn5170@g.skku.edu>
License: MIT
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy==1.26.4
Requires-Dist: pandas==2.2.3
Requires-Dist: scipy==1.13.1
Requires-Dist: scikit-learn==1.6.1
Dynamic: license-file

[![PyPI version](https://img.shields.io/pypi/v/dropbucket.svg)](https://pypi.org/project/dropbucket/)


## dropbucket
Robust SNP-based demultiplexing tool designed to accurately assign cells to donors in pooled scRNA-seq, even under extremely unbalanced pooling condition.

<img src="dropbucket_overview.png" width="800">

## Prerequisites
dropbucket requires the following external tools
- FreeBayes
- Vartrix


## Installation
dropbucket is available through pypi
```
pip install dropbucket
```


## Usage

### From BAM and barcode files
```
dropbucket run -r REFERENCE -b BAM -c CELLBARCODE -k CLUSTERS -o OUTPUT_DIR [-t THREADS]

  -r REFERENCE    reference fasta file
  -b BAM          possorted_genome_bam file
  -c CELLBARCODE  cell barcode tsv file
  -k CLUSTERS     number of clusters
  -o OUTPUT_DIR   output directory
  -t THREADS      number of threads for freebayes and vartrix (default: 1)
```

### From variant matrix files
```
dropbucket clustering -m MTX_DIR -c CELLBARCODE -k CLUSTERS -o OUTPUT_DIR

  -m MTX_DIR      directory containing alt.mtx and ref.mtx
  -c CELLBARCODE  cell barcode tsv file
  -k CLUSTERS     number of clusters
  -o OUTPUT_DIR   output directory
```

## Acknowledgements
This package bundles `fasta_generate_regions.py` from the [FreeBayes](https://github.com/freebayes/freebayes) project.
