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Freyja Wastewater Analysis Series
The GAMBIT_Query_PHB workflow performs taxon assignment of a genome assembly using the GAMBIT task.
Two inputs are required for the GAMBIT_Query_PHB workflow: a genome assembly and a sample name associated with the genome assembly. The default GAMBIT database used for taxonomic identification is version 1.3.0, but alternate GAMBIT databases can be provided
[G](<https://github.com/jlumpe/gambit>)AMBIT determines the taxon of the genome assembly using a k-mer based approach to match the assembly sequence to the closest complete genome in a database, thereby predicting its identity. Sometimes, GAMBIT can confidently designate the organism to the species level. Other times, it is more conservative and assigns it to a higher taxonomic rank.
For additional details regarding the GAMBIT tool and a list of available GAMBIT databases for analysis, please consult the GAMBIT Public Documentation.
The primary output of the GAMBIT_Query_PHB workflow is gambit_predicted_taxon, which is the taxonomic assignment predicted by GAMBIT. The gambit_closest_genomes file indicates the 10 genomes in the GAMBIT database that were most genetically similar to the query genome.
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