Request for including 2x fungal genomes in the GALAXY reference genome list

usegalaxy.eu support
, ,
#1

Dear support team of the GALAXY,

I would like to use Bowtie2 for mapping NGS (ChIP-seq) data for two different microorganism, Aspergillus fumigatus and Verticillium dahliae.

I have already checked for the corresponding reference genomes of these two microbes and they are not available as options in the GALAXY platform.

Would it be possible please to include them in the reference genome inventory?

Please find details of these genomes below:

  1. Aspergillus fumigatus:
    Link:
    https://fungidb.org/common/downloads/Current_Release/AfumigatusAf293/fasta/data/
    File:
    [FungiDB-48_AfumigatusAf293_Genome.fasta]

(https://fungidb.org/common/downloads/Current_Release/AfumigatusAf293/fasta/data/FungiDB-48_AfumigatusAf293_Genome.fasta)

2)Verticillium dahliae:
Link:

ftp://ftp.ensemblgenomes.org/pub/fungi/release-48/fasta/verticillium_dahliaejr2/dna/

File:
[Verticillium_dahliaejr2.VDAG_JR2v.4.0.dna.toplevel.fa.gz]

(ftp://ftp.ensemblgenomes.org/pub/fungi/release-48/fasta/verticillium_dahliaejr2/dna/Verticillium_dahliaejr2.VDAG_JR2v.4.0.dna.toplevel.fa.gz)

Many thanks in advance,

Best regards,

Manolis

1 Like
#2

Hi @Manolis1

Upload the fasta version of each and use them as Custom Genomes “from the history”. You can also promote any fasta to a Custom Build to generate a “database” that can be assigned to datasets (some tools may require that metadata assignment).

There is much prior Q&A about using Galaxy this way that covers the how-to FAQs plus details and other troubleshooting. I added a few tags to your post to help in finding those.

The usegalaxy.eu administrators may write back, if they decide to add the genomes directly. There is a hackathon going on today, so replies may be delayed. But you don’t need to wait – using a custom genome/build is accessible to everyone at all usegalaxy.* servers and most other public Galaxy servers.

Thanks!

#3

Hi @jennaj,

Many thanks for your prompt response and your answer.

Greetings,

Manolis

1 Like