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taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation
https://taxpasta.readthedocs.io/
Apache License 2.0
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Research: list of tools and which taxonomies they support #2

Open jfy133 opened 2 years ago

jfy133 commented 2 years ago

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