How to use Custom Reference Genomes?

A reference genome contains the nucleotide sequence of the chromosomes, scaffolds, transcripts, or contigs for single species. It is representative of a specific genome build or release. There are two options to use reference genomes in Galaxy: native (provided by the server administrators and used by most of the tools) and custom (uploaded by users in FASTA format).

There are five basic steps to use a Custom Reference Genome:

1. Obtain a FASTA copy of the target genome.
2. Use FTP to upload the genome to Galaxy and load into a history as a dataset.
3. Clean up the format with the tool NormalizeFasta using the options to wrap sequence lines at 80 bases and to trim the title line at the first whitespace.
4. Make sure the chromosome identifiers are a match for other inputs.
5. Set a tool form’s options to use a custom reference genome from the history and select the loaded genome.

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{% snippet  faqs/galaxy/reference_genomes_custom_genomes.md %}