Question: Metagenome 16S reference
0
gravatar for agata88
20 months ago by
agata88770
Poland
agata88770 wrote:

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

qiime 16s • 602 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by agata88770

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

ADD REPLYlink written 20 months ago by Brian Bushnell16k

Silva does not have those species too.

ADD REPLYlink written 20 months ago by agata88770

What are these species?

ADD REPLYlink written 20 months ago by Brian Bushnell16k

for example: Bacteroides cellulosilyticus DSM 14838

ADD REPLYlink written 20 months ago by agata88770

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 REPLYlink written 20 months ago by Brian Bushnell16k

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

ADD REPLYlink written 20 months ago by agata88770
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