genomes from quast_downloaded_references in a more general location

[jjkoehorst]

When running metaquast it will download genomes from the NCBI and stores them in the quest output location:

<quast_output_dir>/quast_downloaded_references/

Since we are processing many samples and often have similar genomes but not always I wondered if it would be possible to download them to a generic location in which also other genomes are located? This so that the genomes if present do not have to be downloaded every time.

I checked the documentation but could not find any option related to that. Would it be possible to implement something like this?

[FranckLejzerowicz]

Hello,

I would like to stir this and reinvigorate this question.

In my case, there is not internet on the compute nodes I use and therefore, nothing can be downladed at all.
Hence, being able to have QUAST find pre-downloaded genomes (and SILVA records) would be very interesting

If you could just point to the code locations, I might be able to help develop a solution?

Thanks
Franck