Research: list of tools and which taxonomies they support

[jfy133]

GTDB vs NCBI for example? Fix/non-fixed

Tool	Default Supported	via	profile identifier output formats	Supports raw read counts
MALT	NCBI only (limitation of having to using 0.4 version due to borked LCA in 0.5	custom MEGAN mapping file (0.4: .abin, 0.5 megan*.db	Taxonomy ID Nr. OR Taxonomy name OR Taxonomy path (via megan's rma2info)	☑️
KRAKEN2	NCBI/Greengenes/RDP/SILVA	names.dmp/nodes.dmp/.accession2taxid / Custom taxonomy	Taxonomy name, Taxonomy ID Nr., Path (--use-map-style)	☑️(? fragment == read or just kmer?)
CENTRIFUGE	NCBI	nodes.dmp/names/dmp/.accession2taxid (other taxonomies, same structure)	Taxonomy ID, Taxonomy Name (different files, also supports kraken-style report - although presumably without mpa-style)	☑️
METAPHLAN3	Chochophlan	mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2 (containing NCBI tax ID)	rank, NCBI tax ID	☑️ (with -t rel_ab_w_read_stats)
KAIJU	NCBI	nodes.dmp/names.dmp	Taxonomy ID Nr., Taxon names (via kaiju2table or kaiju-addTaxonNames)	☑️(? fragment == read or just kmer?)
DIAMOND	NCBI	prot.accession2taxid.FULL.gz, nodes.dmp, nodes.dmp	Taxonomy ID	Not directly, only by summarising
MOTUS	NCBI	custom NCBI database file (genomes.tax)	Taxonomy Name, Taxonomd ID Nr., Taxonomy levels	☑️ (-c or -M?)
KrakenUniq	NCBI	Custom taxDB file but has Taxonomy ID, parent, and scientific name	see Kraken (+extra)	☑️(? fragment == read or just kmer?)
Bracken	See Kraken	See Kraken	Taxonomy ID, Scentific Name	☑️

Note tax_from_gtdb.py from GTDB or even