To install the dependencies and create the environment:

. marple-install.sh

This script also adds the functions to run the pipeline in .bashrc.

To concatenate and transfer the fastq files created in MinKnow for pgt or pst:

transfer-pgt <name of experiment> <barcodeXX>=<name of sample> <barcodeYY>=<name of sample> ...
transfer-pst <name of experiment> <barcodeXX>=<name of sample> <barcodeYY>=<name of sample> ...

To run MARPLE:

marple

These functions can be executed from anywhere in the system.

Important

The functions here, assume the reads are in /var/lib/minknow/data/ and marple in /home/$USER/.

Cite this work:
[1] https://doi.org/10.1186/s12864-025-11428-w
[2] https://doi.org/10.1186/s12915-019-0684-y