I've run the latest version of kraken2 with the GTDB 226 database with the --use-mpa-style option to get the same type of report as used with older versions of kraken. However, the report is not recognized by pavian.
It looks like this:
p__Bacillota 185852
p__Bacillota|c__Clostridia 105304
p__Bacillota|c__Clostridia|o__Lachnospirales 33584
p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae 29836
p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea 1604
p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea|s__Mobilitalea sibirica 166
p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea|s__Mobilitalea sp023392995 164
p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea|s__Mobilitalea sp023424995 149
p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea|s__Mobilitalea sp017861355 111
p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea|s__Mobilitalea sp029239365 104
It looks like MetaPhlan output, but with raw counts instead of fractions.
I've run the latest version of kraken2 with the GTDB 226 database with the --use-mpa-style option to get the same type of report as used with older versions of kraken. However, the report is not recognized by pavian.
It looks like this:
It looks like MetaPhlan output, but with raw counts instead of fractions.