Convert MetaPhlAn2 OTU abundance table format to QIIME format. Script set up to work with bacterial-only communities as they are the main subject of our lab, but it could be modified to include all species.
collect_taxonomy.sh script downloads a dump of current NCBI Taxonomy database, converts it to a <Name><TaxIDs><Linage> table and removes all non-bacterial and low-ranked items (e.g TaxIDs for phylums or orders).
Currently everything which is above family level is removed. Ranks that should be saved could be setted inside convert_dmp.pl script in %keep_rank hash.
python3 metaphlan2_to_qiime.py [arguments] script converts MetaPhlAn2 output to QIIME output.
Arguments:
-m, --metaphlan MetaPhlAn2 output (input for the script)
-t, --taxonomy File with NCBI taxonomy
-o, --out Output file in QIIME format