Taxonomy
These classifier tools enable users to assign taxonomy and detect unique genomic signatures.
Apps
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)
Input
These apps take single- and paired-end reads or sets of reads as input.
Narratives
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.
Tutorial Webinar
SFA Collaboration Page
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/.
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