Dear Galaxy team!
Could you put the Arabidopsis thaliana genome in the drop down list?
What kind of data would you need for that, I can help find all the
links from TAIR
Dr. Franziska Turck
Max Planck Institute for Plant Breeding Research
Department Plant Developmental Biology
Group Transcription Control by Chromatin Structure
Carl von Linné Weg 10
Tel: +49 221 5062 246
Fax:+49 221 5062 207
TAIR9 and TAIR10 are available for most tools, with the notable
exception of the new 'NGS: GATK Tools (beta)' tool set. Is this where
you wanted to have the genomes added? For now, only one genome is
available while in beta and using the custom reference genome feature
for other genomes is the current option.
Our plans are to add genomes to the GATK tool set and fill in genomes
for other tools in the near term. I can make sure that the Arabidopsis
genome is included. Normally, we would put as a priority the most
current build, which would be TAIR10. Are other builds of interest?
Links and other information would be great. The source we have used in
the past is (below), please send additions/corrections, help is always
appreciated! The core input is a fasta version of the genome, with
additional related data such as Mitochrondrial, Chloroplast, Plasmid,
etc. as appropriate.
Until this is completed, here are instructions for using a custom
reference genome (available with most tools):
Both species are available for NGS mapping tools (excluding megablast,
which is not intended to host individual genomes on the public
instance). To locate these, including /A. thaliana/, type in 'Arab'
the "Select a reference genome:" box to perform a search. Perhaps
default sort order of the builds list when viewed by scrolling is what
made it appear that only /A. lyrata/ was available (it is the first in
the list and has a different legacy name structure)?
Many people use the main public instance to do NGS mapping every day.
There are significant resources dedicated to this service, but there
usage quotas, limits on job size (72 hr job runtime limit), and delays
during peak usage times (we are experiencing one right now). Your
will determine the best type of Galaxy instance for your purposes.
This wiki has details about Galaxy options:
Hopefully this helps,