Sequence and taxonomy file for GG2

General Discussion
1

Hi! I have 16S full-length reads from PacBio HiFi and planning to evaluate GreenGenes2 using PacBio's Nextflow pipeline for analysis. I wonder where I can download the sequence and taxonomy files for GreenGenes2?

Thanks!

2

Hello @xrobie :wave:

All reference databases and classifiers can be found at the data resources page. Alternatively, you could go to the GreenGenes2 website that was linked to in the paper they published recently. There are several different file types ready for download, and you can pick what you need.

best of luck!

3

Hi @buzic

Thanks! So, I have tried downloading the files from the data resources page as well as the GreenGenes2 website, but it seems that there is a problem accessing the site/files? I had no problem downloading the 13_8 though, but I cannot access the latest release.

Thanks for the help!

1 Like
4

@xrobie ,

You are correct, I also can't access it at the moment either - seems it could be something at their end.

5

@buzic ,

Is it possible to access these files somewhere else?

Thanks!

6

Hi @xrobie,

Thanks for reaching out and bringing this to our attention!

We recently moved the location of our latest classifiers, and this got missed when adding the new URLs to our data resources page. I've just submitted a fix for this, but in the meantime here are the direct links you can use:

Greengenes2 2022.10 full length sequences
Greengenes2 2022.10 from 515F/806R region of sequences

Apologies for any confusion caused by this! Let us know if you run into any other issues.

Cheers :lizard:

3 Likes
7

Hi @lizgehret :wave:

Thanks! It's working now.

Regards to everyone~

3 Likes
8

Hi @xrobie,

We were performing network maintenance earlier in the week as well, which resulted in some downtime for the Greengenes2 FTP.

Best,
Daniel

1 Like
9

Thank you @wasade ! I will check the site again.