What this entity is
Canonical name: Centrifuge. 1
Known aliases: No aliases were reported in this document. 1
Stable external identifier: None was reported in this document. 1
Centrifuge is a taxonomic classification method used among the native NMDC read-based classification outputs. 1
Key facts from the documents
In the earlier NMDC deployment, Centrifuge produced approximately 0 domain-level Eukaryota signal because its reference database was prokaryote-restricted. 1
Centrifuge therefore did not provide a usable estimator of eukaryotic fraction for that analysis, unlike the eukaryote- and plastid-aware GOTTCHA2 classification. 1
In the NMDC community-metabolic-ecology deployment, approximately 1,352 Centrifuge taxa matched multiple GTDB clades within the same genus; one representative clade was selected by alphabetical tiebreaking on gtdb_species_clade_id, and these genus-proxy-ambiguous taxa accounted for approximately 6.5% of mapped abundance. 2
This refines the earlier database-compatibility limitation: even when Centrifuge taxa support broad community-to-pangenome mapping, genus-level ambiguity can affect which GTDB species-clade pathway records are assigned. 2
The result illustrates that classifier databases were not interchangeable for eukaryote quantification in the Metadata Correlates of Eukaryotic Contamination in NMDC Prokaryote-Targeted Metagenomes analysis. 1
This limitation is relevant to multi-omics-integration, because integrating read-based taxonomic results with environmental metadata requires checking whether each classifier and database can detect the target domain. 1
Centrifuge was evaluated alongside kraken2 in the NMDC classification workflow, while GOTTCHA2 supplied the usable eukaryotic-fraction response variable. 1