dropbucket 2.1.1

Robust SNP-based demultiplexing tool

dropbucket

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

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 project.