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Metagenome 16S reference

Hi all!

I was testing different references (gg_13_8, gg_13_5) for the occurrence of several species and I saw that most of them are missed . I would like to add those sequences manually. The main problem is how to add it to make it compatible with qiime?

PS. How greengenes database is made?

Thanks in advance!

Best, Agata

16s qiime
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written by agata88 agata88

Greengenes has not been updated in a long time. I suggest you try Silva.

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written by Brian Bushnell Brian Bushnell

Silva does not have those species too.

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written by agata88 agata88

for example: Bacteroides cellulosilyticus DSM 14838

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written by agata88 agata88

I ran this:

zcat SILVA_128_SSURef_tax_silva_trunc.fasta.gz | grep cellulosilyticus

and got many entries. Among them:

>ACCH01000108.3638.5148 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides cellulosilyticus DSM 14838

So, it looks like it is present.

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written by Brian Bushnell Brian Bushnell

hmm, yes indeed. I was using Silva124 version not the one you have used. I am gonna go with 128 version. Thanks.

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written by agata88 agata88

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