Kraken.txt

Kraken suite is an end-to-end pipeline for the classification, quantification, and visualization of metagenomic datasets. (https://www.nature.com/articles/s41596-022-00738-y)

The protocol describes two scenarios:

(1) quantification of the species in a given metagenomics sample;
(2) detection of a pathogenic agent from a clinical sample.

Tools Included: Kraken2, KrakenUniq, Kraken, Kraken2Uniq (based on KrakenUniq and included in the Kraken 2 codebase), Bracken (to compute species abundance), KrakenTools and Pavian (downstream statistical analysis and visualization of the
classification and abundance estimation results). 

Kraken, Kraken2, Kraken2uniq, Krakenuniq - Methods differ in the ways they count, access, and store the k-mer information,


Alpha_diversity can be used to quantify the diversity in a sample, and beta_diversity can be used to compare diversity across samples.

Bracken - Provides estimated reads per species in the sample.
Kraken 2 can also classify reads against protein databases using six-frame translation.

Remember: The entire microbial biosphere is still far from being completely sequenced, and thus missing or partial genomes may introduce biases and reduce classification performance.

Refer: https://github.com/jenniferlu717/KrakenTools
Refer: https://bioconda.github.io/recipes/krakentools/README.html
Refer: https://ccb.jhu.edu/software/kraken/MANUAL.html