Taxonomy
These classifier tools enable users to assign taxonomy and detect unique genomic signatures.
Last updated
These classifier tools enable users to assign taxonomy and detect unique genomic signatures.
Last updated
GOTTCHA2 (Genomic Origin Through Taxonomic Challenge): Uses a novel taxonomic profiling method for metagenomes that is both gene-independent and signature-based. It significantly reduces false discovery rates (FDR).
Centrifuge Taxonomic Classifier: Enables rapid, accurate, and sensitive labeling of metagenomic reads and quantification of species. (Beta-only)
Kraken2 Taxonomic Sequence Classifier: Examines the k-mers within a query sequence and maps k-mers to the lowest common ancestor (LCA) of all genomes in the reference database known to contain a given k-mer. (Beta-only)
These apps take single- and paired-end reads or sets of reads as input.
GOTTCHA2 webinar – demonstrates Genomic Origin Through Taxonomic CHAllenge apps using example data.
Created and made public by Mark Flynn of Los Alamos National Laboratory.
Metagenome-Assembled Genome Extraction from a Compost Microbiome Enrichment – for more on how to create metagenome-assembled genomes.
Kaiju – a similar taxonomic classification app.
These apps were developed as part of the Bacterial-Fungal Interactions SFA at LANL. To learn more about this collaboration, see: https://www.kbase.us/chain-sfa/.