scAVENGERS

scAVENGERS is a pipeline for clustering cell barcodes in multiplexed single cell ATAC-seq sequencing data. scAVENGERS achieves high performance through two strategies.

  • Tolerant variant calling to resolve sparseness of scATAC-seq data

  • Probabilistic modelling on how genomic DNA fragments are incorporated into scATAC-seq reads

Running scAVENGERS

  1. Clone the repository and install dependencies.

wget https://github.com/kaistcbfg/scAVENGERS/archive/refs/tags/v0.1.0.tar.gz
tar -xvzf v0.1.0.tar.gz
conda env create -f scAVENGERS/envs/environment.yaml

  1. After you cloned the repository, you can run scAVENGERS by executing the command below.

$SCAVENGERS_DIRECTORY/scAVENGERS [pipeline|cluster] [options]

scAVENGERS modules

scAVENGERS provides some modules to aid demultiplexing single cell DNA sequencing data.

  • scAVENGERS pipeline: scAVENGERS pipeline is a whole pipeline for demultiplexing single cell ATAC-seq data.

  • scAVENGERS cluster: scAVENGERS cluster is a module for clustering cell barcodes in a multiplexed single cell ATAC-seq data.

citation

TBD

Future update plans

The feature below may be updated in future.

  • Module for assigning clusters to donors, given reference variants

  • Supporting heterogenous ploidy for each cell and genomic region

  • Developing generative model for doublet and ambient variant detection

  • Some additional optimizations