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

Tutorial webinar presented by Mark Flynn of Los Alamos National Laboratory

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/.