Metagenome 16S reference

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6.8 years ago

agata88 ▴ 870

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 • 1.5k views

ADD COMMENT • link 6.8 years ago by agata88 ▴ 870

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

ADD REPLY • link 6.8 years ago by Brian Bushnell 20k

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Silva does not have those species too.

ADD REPLY • link 6.8 years ago by agata88 ▴ 870

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What are these species?

ADD REPLY • link 6.8 years ago by Brian Bushnell 20k

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for example: Bacteroides cellulosilyticus DSM 14838

ADD REPLY • link 6.8 years ago by agata88 ▴ 870

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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.

ADD REPLY • link 6.8 years ago by Brian Bushnell 20k

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

ADD REPLY • link 6.8 years ago by agata88 ▴ 870

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