Qiime 2 Biom File format


#1

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,

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Faecalibacterium;s__prausnitzii

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 ?


#2

Hello,
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!


#3

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


#4

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!


#5

table.qza (48.1 KB)


#6

taxonomy.qza (60.7 KB)