# Taxonomy

## Apps

* [GOTTCHA2 (**G**enomic **O**rigin **T**hrough **T**axonomic **Cha**llenge)](https://kbase.us/applist/apps/gottcha2/run_gottcha2/release): 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](https://narrative.kbase.us/#catalog/apps/centrifuge/run_centrifuge/beta): Enables rapid, accurate, and sensitive labeling of metagenomic reads and quantification of species. *(Beta-only)*
* [Kraken2 Taxonomic Sequence Classifier](https://narrative.kbase.us/#catalog/apps/kraken2/run_kraken2/beta): 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](https://docs.kbase.us/data/upload-download-guide/reads) or sets of reads as input.

## Narratives

* [GOTTCHA2 webinar](https://narrative.kbase.us/narrative/88330) – 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](https://narrative.kbase.us/narrative/33233) – for more on how to create metagenome-assembled genomes. 
* [Kaiju](https://narrative.kbase.us/legacy/catalog/apps/kb_kaiju/run_kaiju/release) – a similar taxonomic classification app.

## Tutorial Webinar

{% embed url="<https://www.youtube.com/watch?v=N-_89NJu9So>" %}
Tutorial webinar presented by Mark Flynn of Los Alamos National Laboratory
{% endembed %}

## 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/](https://www.youtube.com/redirect?event=video_description\&redir_token=QUFFLUhqbG8yUEZKNE9FN3ZmbnNVdjIwNE5xUlBESFZnd3xBQ3Jtc0ttU1FPR0U3UU55dmRmUFJWd0piS0NMcE8zNVM5SHBFS1o0SFRBendmeW1TQTNlREdJQVlmNE5KTUhpaWFyR3MtR2w5N2xjckxvRF9fdVVwbzNRYnE2VnJCUWxxZVVJMjNWQlpwMkRoeElvbEFXbUhETQ\&q=https%3A%2F%2Fwww.kbase.us%2Fchain-sfa%2F\&v=N-_89NJu9So).