request for tomato genome version SL4.0

1

Hello,

I would like to request adding the latest tomato genome assembly to Galaxy Main.

The latest genome assembly is called “SL4.0” and also S_lycopersicum_Feb_2019.

Here is the sequence from the tomato genome Web site:

ftp://ftp.solgenomics.net/tomato_genome/assembly/build_4.00/S_lycopersicum_chromosomes.4.00.fa.gz

Many thanks,

Ann Loraine (IGB project)

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2

This is to reinforce the request made by Ann. Please add the SL4.0 version of tomato genome to Galaxy!

3

Hi,

sorry for the late reply. We install this Tomato genome on usegalaxy.eu

Cheers,
Bjoern

4

I am sorry to insist, but I think the SL4.0 version of tomato genome is not in Galaxy yet. Could you please include it… Thank you so much in advance.

Cheers,
tania

5

Hi @Tan_H

For now, the genome is available at UseGalaxy.eu for most tools. Please double check, and if a specific tool seems to be missing the assembly, please post back the tool name/version and we can followup more to come up with a temporary workaround. :slight_smile:

The other public usegalaxy.* servers will likely host this index, and many other requested indexes, by the end of this year. Part of that work includes adding in entirely new genomes but also filling in gaps.

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6

Could you install this tomato genome on Galaxy Australia as well, please? Many thanks.

7

Hi @YiJie_Wang

The UseGalaxy servers will have all reference indexes synched up soon.

We can ask about this genome specifically but I think the answer will probably still be “soon but not immediately”. Hi @igor – what do you think?

Meanwhile, for immediate use, you can use any reference genome as a Custom Reference Genome. See posts with this tag custom-genome. Try sorting the searched topics by date to find the most recent updated instructions.

Or, you can use the server where the genome is hosted. It is fine to have an account at each server – this grants you more quota space, too!

You don’t have to start completely over since it is easy to move data between servers without a download step. Everything happens by URL. How to → FAQ: Transfer entire histories from one Galaxy server to another.

Hope this helps! :slight_smile:

8

Hi @jennaj,

I wish the ref data will be synched up across UseGalaxy servers!

We received a request for the tomato genome, v.4. NCBI still lists v.3 as the reference assembly, and v.5 is available, plus the GA team is busy with GTA :frowning: I don’t know how long it might take. We rarely add new ref genomes lately.

I’d recommend a custom ref genome in a history.

Kind regards,
Igor

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