This is a really helpful post and I am trying to do similar to the OP. Basically, I would like to run DIAMOND against NCBI nr database. Based on this helpful thread, I am hoping to import the pre-indexed NR database from the link you provided: ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*tar.gz into my Galaxy instance.
Then, I hope to run DIAMOND on Galaxy with the following fields:
- “What do you want to align” --> Align DNA query sequences (blastx)
- “Input query file” --> I’ll input contig .fastq of metagenomic data
- “Will you select a reference genome from your history or use a built-in index?” --> I guess I would say “use one from my history” and then select the NCBI nr file that I imported
I am not sure how accurate my pipeline is, but tentatively I have two questions that I would be so grateful to hear advice about:
It seems from this post that public and usegalaxy platforms cannot accomodate this analysis. Of the platforms you listed (https://galaxyproject.org/choices/), would any (free options) support my tentative pipeline? I may not have access to “Academic Cloud Services” because I am a postdoctoral scholar at a University in Japan. It seems “TIaaS” may be an option and I can apply (worried if I would be accepted) but would it even be suitable for this purpose? I would appreciate so very much any advice on which platform to possibly focus on.
Does my pipeline even seem possible?
Thank you for any input.