MEGAN can now import the lastest BIOM format (2.1)

I have implemented a first version of BIOM2 format support. This is the format that QIIME now uses. You will be able to open any file ending on .biom, whether it is in BIOM1 format (the original BIOM format, based on JSON) or BIOM2 (a new version of the format that is based on HDF5).

QIIME reports taxonomic assignments in a “path format” that looks like this:

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

During import, MEGAN needs to decide which NCBI taxon this should be mapped to.

MEGAN provides a choice of two algorithms for doing this:

  • Match taxonomic path. In this mode, MEGAN will place this assignment onto the most specific taxon whose path in the NCBI taxonomy contains the QIIME path.
  • Match most specific node. Matches the most specific node regardless of whether the path is preserved.

Because a path reported by QIIME does not always match the path in the NCBI taxonomy, in practice the first choice is more conservative, while the second choice is more specific.

Unfortunately, the BIOM format is underspecified and there are no examples for many of the indicated features of the format, so the current in MEGAN is incomplete.

If you have any problems loading your biom files into MEGAN then please let me know and I will extend MEGAN’s BIOM2 parser accordingly.

2 Likes

Hi Daniel!
I’ve been trying to import a biom file generated using Qiime2 (2018.11) but keep experiencing this error: “Execute failed: java.io.IOException:invalid type:”

Any idea why this error might be occurring as MEGAN should be fine with biom2 files.

Biom2 is a moving target and this might be the reason why the MEGAN parser breaks. If you give me access to such a file then I will try to debug this.

Hi Daniel I am knew to the community.
I am facing the same kind of problem as stated above. Actually I have both QIIME1 and QIIME2 generated files (.biom and Featuretable) and I want to generate a phylogenetic tree in MEGAN. When I import QIIME1 .biom table to the MEGAN I get an error as I took its screenshot below. Also I am attaching my qiime1 biom table herefiltered_otu_table.biom (2.3 MB)

Hi Daniel, apologies for a delayed response. I do not require anymore to parse the biom file, however if you want I can still share one for you to debug (obviously in case you want to and it will be helpful).

Yes, please send it to me by email

Sent the file to your university email.

Datenschutzerklärung