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Bacterial community profiling using 16S rRNA nanopore sequencing

Hello! I am working on characterizing soil microbiome using full-length 16S rRNA gene amplicons generated through nanopore sequencing. I have already done the taxonomy assignment part and stuck with how am I going to proceed to downstream analysis. How do I perform taxonomic composition analysis if I want to know the relative abundance profiles of taxa at different taxonomic levels (e.g., genus, family, and phylum)? Should I create different count tables for such levels and run separate analyses?

nanopore full-length microbiome emu 16s-rrna
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updated by michael.ante michael.ante • written by Cedrick • Cedrick

Hi,

No, you definitely do not need to create separate count tables. You should keep one master ASV/OTU count table and let your downstream software do the grouping.

May I ask are you using QIIME?

If you are, you don't need to create separate count tables. The following will give you for all hierarchy level.

qiime taxa barplot --i-table table.qza --i-taxonomy taxonomy.qza --m-metadata-file sample-metadata.tsv --o-visualization taxa-bar-plots.qzv

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written by Bruntland Aldre • Bruntland Aldre

He is using emu, not qiime

In emu count table features are taxonomic labels (p__Phylum;c__Class;o__Order;f__Family;g__Genus;s__Species) not ASV. qiime taxa barplot could work but he must add a fake_id to each taxonomic labels before converting the emu count table as table.qza

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written by andres.firrincieli andres.firrincieli

1 answer

Hi,

On the EMU Git-hub, they reference the following downstream workflows:

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written by michael.ante michael.ante

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