CellTag-tools: Computational framework for Clonal analysis

CellTag-tools is a highly scalable and efficient software package for analysing multi-modal single cell lineage tracing data available on GitHub. Read more about CellTagging at Jindal et al. Nat. Biotech. (2023) , Kong et al. Nat. Protocols (2020), and Biddy et al. Nature (2018)

CellTag-tools identifies clonal relationships within single-cell datasets, starting from CellTag reads enabling insights into cellular lineage and dynamics.

Key Features

• CellTag Read Extraction Extracts CellTag sequences from single-cell BAM files.
• Error Correction and Filtering Refines CellTag data for high accuracy downstream analysis.
• Clone Identification Identifies clonal populations based on shared CellTag signatures.

Workflow Overview

1. Parsing Single-Cell BAM Files Extract CellTag sequences from BAM files, supporting pipelines like CellRanger and CellRanger-ATAC.
   • Requirements:
     • Sample configuration file (specifies sample details, paths, cell barcodes, assay types, CellTag versions).
     • A pipeline processes the samples, as outlined on our GitHub repository.
2. Processing CellTag Reads to Identify Clones After parsing, the tool performs:
   • Filtering and Error Correction Filters out low-quality reads and corrects sequencing errors.
   • Allowlisting Validates CellTag sequences using predefined lists.
   • Matrix Construction Constructs cell-by-CellTag matrices, which are filtered and binarized.
   • Clone Calling Identifies clones based on shared CellTag patterns using similarity matrices.

Installation

To install the package, clone the repository and use pip:

# Clone the repository
git clone https://github.com/jindalk/celltag_tools.git

# Navigate to the repository
cd celltag_tools

# Install the package
pip install .