Building a custom reference for kb-python in a virtual environment

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Building a custom reference for kb-python in a virtual environment

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Last edited Feb 25, 2021

Created on Nov 25, 2020

This example demonstrates a shell script that builds a custom kb-python reference index for single-cell RNA-seq analysis. It shows the step-by-step process of creating a Python virtual environment, installing kb-python, and downloading Gencode mouse reference files. The script then appends custom FASTA and GTF sequences to the standard reference using `cat`, and constructs the index via the `kb ref` command with the `--workflow standard` flag. The code relies on the `venv` module, `pip3`, `wget`, and `gunzip` to prepare files, and explicitly requires properly formatted FASTA headers and GTF entries for successful integration.

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