This is a list of genomes that have been suggested for support in Galaxy.
These are mostly large reference sequences that require lots of time and disk space to index for mapping tools.
The table shows whether the index has been generated for the galaxy tool:
- dev - indicates the index has been generated
- test - the index is available on the staging instance of galaxy and being tested
- PROD - the index is available on the production Galaxy and is available to all users
( Many genome applications build a special index into the reference genome in order to perform mapping. Building such an index occurs once and may take hours for a large genome sequence, but allows sequences to be mapped quickly. )
If there is a large genome you need, send an email to email@example.com
subject: Galaxy genome request <genome name>
URL for the genome source (preferably a single fasta with a sequence for each chromosome)
( These requests require changes to the galaxy configuration and a restart of galaxy, so requests may take several weeks. )
For smaller genome sequences such as bacterial, archeal, small fungal, or viral genome sequences you can either upload the sequence yourself, or request MSI to add the reference to the "Shared Data" library, which you could then import to your history. Most tools allow you to select references from your history as well as the "built in" or "locally cached". Building a bowtie index for a bacteria-sized genome only requires seconds of time, so it can be done on the fly.
You might want to do create a "Custom build" when using a genome reference from your history. This allows to set the Database/Build attribute of datasets to your custom build name, and to use that name for visualizing results in the galaxy Track browser. Under the "User" menu tab, select "Custom builds" and create a "Custom Database/Build" entry for this genome reference. You will need a 2-column file that gives the name of each chromosome/contig in the reference assembly and the base pair length of that sequence. You can use the "Compute sequence length" tool in the "FASTA manipulation"
category to generate the Chromosome length file.