adding Bacillus Licheniformis genome builds to customprodb + HISAT2

Hi Galaxy team,

I would like to use HiSat2 and customproDB for proteomics of Bacillus Licheniformis. Under Reference Genome there is a note “If your genome of interest is not listed, contact the Galaxy team (–genomeDir)”. If this is not the right contact, kindly redirect me.

Thank you.

1 Like

Hi @brandonkarbs34

For smaller genomes, we usually recommended the Custom Genome/Build functionality. In short, upload your genome fasta file, confirm/normalize the format, and use the standardized fasta dataset with tools as a reference genome from the history. Optionally, also promote your custom genome to a custom build to have your data work with more tools. Custom builds can be assigned as a “database” to datasets – and some tools interpret that metadata.

FAQ: * Preparing and using a Custom Reference Genome or Build

Note: The tool CustomProDB does not appear to have any annotation indexes natively available and might never have any created. You’ll need to find reference annotation that matches your reference genome (whether a built-in genome index exists for other tools or not).

FAQ: * Mismatched Chromosome identifiers (and how to avoid them)

Formatting custom reference genomes correctly and ensuring a proper match with whatever reference annotation is used are both very important actions to take when setting up an analysis. If not done, expect tool errors or scientific content issues that will not resolve until the reference data are corrected/matched.

Hope that helps!