Downloading 16S sequences using JGI portal

Question

[chrystiam.sossa]

Hi everyone, Do you know if there a way to download 16S sequences for a specific collection of the https://jgi.doe.gov/. I want to download al 16S sequences for this collection https://genome.jgi.doe.gov/portal/TheHunmicrobiome/TheHunmicrobiome.info.html in order to be used in the DADA2 pipeline and picking OTUs

Many thanks,
Chrystian

Answer 1

[pfchuckran]

Just in case anyone is facing a similar problem 3 yrs later: You could locate this study on IMG and then, using the following description from the 2021 IMG publication, access just these sequences:

As an example, consider a query to retrieve all 16S rRNA genes longer than 500nt in the freshwater sediment metagenomes in IMG. First a user would identify all freshwater sediment metagenomes in IMG, which can be done using the Advanced Search Builder in Genome Search and the following query conditions:

Taxonomy – Domain: *Microbiome

Study Dataset Names – Genome Name / Sample Name: Freshwater

Environmental Classification – GOLD Ecosystem Type: Sediment

This Genome Search query retrieves a total of 22 metagenomes, which can be selected and added to the Genome Cart. In order to find all 16S rRNA genes longer than 500nt in these metagenomes a user would go to the Advanced Search Builder in the Gene Search interface and add the following query conditions (Figure 2A):

Gene Model Attributes – Locus Type: rRNA_16S

Gene Statistics – Gene Amino Acid Length: > 500

and add all metagenomes in the Genome Cart to the set of ‘Selected Genomes.’ The query retrieves 131 16S rRNA genes (Figure 2B), which can be selected and added to Gene Cart for further analysis. Gene Cart also allows exporting selected gene sequences in a FASTA format. Similar to the Genome Search interface, Gene Search also records all search history to allow users to view and to reuse their previous queries (Figure 2C).

You could then export the sequences by adding them to your cart and going to the export tab.

Answer 2

[Arup Ghosh]

To download the data first you have to create a JGI account. Log in to your JGI account navigate to TheHunmicrobiome and click on the Download link and after accepting the data usage policy you will be redirected to the following page.

Then use of any of the methods mentioned in the following article to download all the datasets.

https://genome.jgi.doe.gov/portal/help/download.jsf

[chrystiam.sossa]

Hi Arup, thanks for the information. I did in that way, but that way is to download complete genomes, the sequencing reports. etc... I want just the 16S rDNA sequences for the bacterias isolated there.

Kind regards,

Chrystian