How can i identify the core microbiome using qiime2 ?

Dear all,

When i used qiime1 i performed core microbiome analysis using the following command line :
compute_core_microbiome.py -i otu_table.biom -o otu_table_core

What is the equivalent of this command line in qiime2 ?

Thanks

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Hey there,
See if it would help you:
qiime feature-table core-features --help

All the best

Hi @lca123,

Thank you for the response.

  1. Can you give me details about this option --p-steps :
    –p-steps INTEGER The number of steps to take between min-fraction and
    Range(2, None) max-fraction for core features calculations. This
    parameter has no effect if min-fraction and
    max-fraction are the same value. [default: 11]
    Why they put default 11. What are the steps required for calculations ?
  2. when i calculated core microbiome i found feature such as
    3f81af840a34fe5c683a531aff72fe7be5b0ef30
    What can i do to find the corresponding bacterial taxa ?

Thanks

If I well understodd, those steps are just how many calculations de script will run for understanding if a feature is a core-feature or not.
You have found this hash-id because you’re working with a feature-table, so there are no taxa identification there. You have to run a classification against a database to find bacteria taxa for those features.

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@lca123

Thanks for the response. I performed classification against a database qza and qzv files were generated. in qzv file when i looked to the table i didn’t find hash id and its correspondance taxa i find directly the taxa i need to see the corresponding taxa for each hash id does the biom table display those informations ? how can i open the biom file using qiime2 ?

Hi @M_F - the feature ID should’ve been in your taxonomic classification output. If it wasn’t, then that suggests to me that maybe you mixed up some of your files. Maybe go back and double-check?

Dear @thermokarst

Thanks for the response. How can i open a biom file using qiime2 script ?

Thanks

Please see the “exporting” tutorial:

https://docs.qiime2.org/2020.8/tutorials/exporting/

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