Qiime 2 Biom File format


I have been trying to import a BIOM file output from QIIME 2 into MEGAN and had no luck. I understand the OTU IDs are in the first column (when converted to TSV) and they can be in the following format,


It is also my understanding that the BIOM file from QIIME 1 had the Greengenes IDs in the first column. So can MEGAN read Greengenes IDs to interpret taxonomy and do I also need to format my ouput from QIIME2 to have greengenes IDs just like Qiime1 ?


May I extend this question: Is there any possibility that the QIIME2 artifact files (e.g. FeatureTable[Frequency] and FeatureData[Taxonomy]) can be imported to Megan6 directly?

Best regards!


could you supply me with example files as a starting point?
I will then dig into this.


Here are two files, one FeatureTable[Frequency] and one FeatureData[Taxonomy], that I took from the Qiime2 tutorial “Moving Pictures”.

The files are also available there (Qiime2 calls these compressed files ‘artifacts’):
The table artifact under section “Option1 DADA2”
The taxonomy artifact under section “Taxonomic Analysis”.

I thought it might be better for you to use these files as there is plenty of info available on theses great tutorials about creating theses files.

PS: I realized that I can add only a limited number of files to my reply; so the two files are in two independent subsequent replies. Sorry for that inconveniance!


table.qza (48.1 KB)


taxonomy.qza (60.7 KB)