The Persona shell consists of a simple command parser and set of Python submodules that implement common bioinformatics tools using Persona's TensorFlow-based dataflow framework.

Before continuing, make sure you have installed the Persona System and entered the virtual environment:

source path-to-persona-system/python-dev/bin/activate

The persona Python script is the entry point to the Persona environment. You may want to add it to your PATH. Use persona -h to get a list of all available functions.

First, you will probably want to import a dataset. Persona operates on the AGD format, which is efficient and allows for seamless scale-out distribution. Use one of the import functions to import your data, for example:

persona import-fastq --paired -p 4 --compress-parallel 6 -w 2 -o <output_directory> -n my_dataset file_1.fastq file_2.fastq

will import a paired FASTQ dataset into an AGD dataset called "my_dataset". Use persona import_fastq -h to see what all the options are for. Generally, many will control parallelism at the IO read, compute, and IO write stages. You can tweak these numbers to get better performance.

The output_directory will now contain your paired dataset in AGD format.

To display ranges of records in the terminal you can use the display command

persona display 0 7 -d <dataset_directory> <dataset_directory>/metadata.json

This can be useful for sanity checking results.