Diversity Analysis of WGS data in QIIME2

User Support
1

Hi,

I am analyzing WGS using metaphlan2 and humann2. But there are not various alpha and beta diversity measures that can be estimated like QIIME pipeline. Is there an intermediate file from this WGS analysis that can be used in QIIME2 pipeline to obtain alpha and beta diversity?

Thank you,
Best,
R

2

Hello @rr220,

What is the structure of your data currently? Would it fit conceptually into a feature-table like format?

3

I have it as a merged abundance table in Excel. Paste below. Can this be used? Also what would be the script to run this?

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4

Hello @rr220,

That looks a frequency data, is that correct? If so you can use the FeatureTable[Frequency] import type.

The workflow is basically as follows:

  • save that as a tsv file
  • convert it to a biom table using biom convert -i <your tsv> -o <your biom> --to-hdf5
  • import it as a feature table frequency using:

qiime tools import --input-path --type 'FeatureTable[Frequency]' --input-format BIOMV210Format --output-path

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6

You could also take a look at this plugin that I created, q2-sapienns, which assists with importing data that was generated from Humann and metaphlan into QIIME 2 artifacts for downstream analysis.

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7

Thank you for your suggestion and help

8

Thank you for your suggestion and help

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