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Old 10-31-2012, 12:35 PM   #1
Location: italy

Join Date: Apr 2012
Posts: 45
Default analyze 16S metagenomic 200bp data to species level

Hi everyone,
i've got 200bp metagenomic data based on V3 region and i'm currently using QIIME to analyze it... but i reach family level by default.

I would like to reach species level if possibile, or at least try it... so i've found in the QIIME forum a modified version of the RDP taxonomic table that allow to assign taxonomy to the OTUs down to species level, but it worked for only 5% of my sequences, wile the remaining 95% stopped at genus or even family level.

I'm not a big expert in metagenomics, can you suggest me other tools that i can try in order to analyze my data down to species level and see if i can reach better results?
Gorbenzer is offline   Reply With Quote
Old 11-01-2012, 08:11 AM   #2
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Location: Ohio

Join Date: Jan 2010
Posts: 144

NCBI has a 16S database with all named type strains that you can BLAST against, though I would think if you got a high identity match to that the classifier should be able to predict it.

Another approach would be to identify full length sequences corresponding to your OTUs, then make trees with them and named species and infer the taxonomy from that.
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Old 11-06-2012, 12:11 AM   #3
Location: Leiden, The Netherlands

Join Date: Sep 2012
Posts: 28

If you have the funding I'd say try MEGAN, much easier to use and more accurate. If you don't have the funding you could always ask for periodical license (45 days) to use and try it and then say that you are not going to use it after all.
RickBioinf is offline   Reply With Quote
Old 11-06-2012, 07:06 AM   #4
Location: Flagstaff, AZ

Join Date: Feb 2010
Posts: 51

I assume that when you say "metagenomic data" in this context, you mean you have 16S rRNA data from mixed microbial communities.

If you are interested in species, you might check out speciate-it

It uses markov models to try and mine down to finer taxonomic levels.
themerlin is offline   Reply With Quote

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