Are there any methods to retrieve and download 16S rRNA gene sequences from a large number of metagenomes at once?

[Ilnam Kang]

Hi,

I've been trying to retrieve and download 16S rRNA gene sequences from a large number (>500) of metagenomes at once.

Below is the approach I've been doing. 

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(After adding metagenoms into the Genome Cart)
Find Genes -->

Gene Search -->

Advanced Search Builder -->

Enter "Bacterial SSU" for Gene Product Name (inexact)

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But, in this way, the number of metagenomes that can be searched is capped at 50. Further, if the number of 16S rRNA genes retrieved from the metagenomes exceeds 20000, I cannot add all these 16S rRNA genes into Gene Cart for export. So, I think this approach would take much time and effort for a large number of metagenomes.

Are there any convenient ways to download 16S rRNA gene sequences from a large number of metagenomes?

Thanks.

[Ken Chu]

You can download IMG's data set from the JGI Portal

https://genome.jgi.doe.gov/portal/

The Portal has a API for bulk downloads.

-IMG