Pycashier

Tool for extracting and processing DNA barcode tags from Illumina sequencing.

Default parameters are designed for use by the Brock Lab to process data generated from ClonMapper lineage tracing experiments, but is extensible to other similarly designed tools.

Documentation

See the documentation for more in-depth installation and usage instructions.

Getting Started

Installation

Conda

You may use conda, mamba, or micromamba to install pycashier and it's runtime dependencies.

micromamba install bioconda::cutadapt bioconda::fastp bioconda::pysam bioconda::starcode conda-forge::pycashier

You can also use the included env.yml to create your environment and install everything you need.

wget https://raw.githubusercontent.com/brocklab/pycashier/main/conda/env.yml
micromamba create -f env.yml
micromamba activate cashierenv

Additionally, you may use pixi to install and use pycashier.

pixi init --channel conda-forge --channel bioconda myproject
cd myproject
pixi add pycashier starcode pysam cutadapt fastp
pixi shell

Docker

If you prefer to use use docker you can use the below command.

docker run --rm -it -v $PWD:/data -u $(id -u):$(id -g) ghcr.io/brocklab/pycashier

Note

You should specify a version tag with the image for better reproducibility for example, ghrc.io/brocklab/pycashier:v2024.1001.

Usage

To extract barcodes from targeted sequencing data:

pycashier extract -i fastqs -o outs

To combine data from multiple samples and compute basic overlap metrics:

pycashier receipt -i outs -o combined.tsv

See pycashier --help and pycashier SUBCMD --help for additional subcommands and options.

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Pycashier is open source and licensed under the MIT License.