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.
See the paper for a high-level overview and the documentation for more in-depth installation and usage instructions.
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::pycashierYou 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 cashierenvAdditionally, 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 shellIf 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/pycashierNote
You should specify a version tag with the image for better reproducibility for example, ghrc.io/brocklab/pycashier:v2024.1001.
To extract barcodes from targeted sequencing data:
pycashier extract -i fastqs -o outsTo combine data from multiple samples and compute basic overlap metrics:
pycashier receipt -i outs -o combined.tsvSee pycashier --help and pycashier SUBCMD --help for additional subcommands and options.
Pycashier is open source and licensed under the MIT License.