Metaphlan4- can I keep the NCBI_tax_id in the merged_abundance_table?

Hi!
I just have a simple question about the merged_abundance_table for metaphlan4.

The merged profile table of metaphlan3 has a column, NCBI_tax_id. However, this column has disappeared in Metaphlan4. The individual profile table still has the NCBI_tax_id column.

Is there a way to keep the NCBI_tax_id in the merged profile table in Metaphlan4?

Thank you very much!

Keehoon

Hi @Keehoon_Lee
In Metaphlan 4, for the ~5k unknown SGBs (uSGBs) included in the database, there is not a correpondance with the NCBI taxonomy database. For this reason and to avoid inconsistencies when a taxonomic species (e.g. F. praus) spans multiple SGBs (and thus they receive the same NCBI tax id), from version 4.0.3 we decided to remove this field from the merged profiles. However, you can still download the previous script from here: MetaPhlAn/merge_metaphlan_tables.py at b78e5b895125dca35330a79695876d7299fd974a · biobakery/MetaPhlAn · GitHub

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