Chapter 7 Kraken2
Kraken2 is a highly efficient, open-source taxonomic classification system designed for metagenomic sequence data. It utilizes exact k-mer matches to classify sequences by comparing them to a database of known genomes, providing accurate and rapid identification of microbial taxa. Kraken2 is widely used in microbiome research for analyzing complex microbial communities, enabling researchers to classify millions of sequences in a matter of minutes. Its performance and accuracy make it a valuable tool for large-scale metagenomic studies, pathogen detection, and environmental microbiology.
7.1 Use Kraken2
Kraken2 is already installed. To copy Kraken2 binaries to your personal bin directory, run the following command:
Check the Version: Run the following command to check if Kraken2 is installed and to see the version number:
7.2 Available Kraken2 Databases
Some Kraken2 databases are available in the Group Directory. These databases can be found under the following directory:
/mnt/vstor/SOM_PQHS_LXZ716/Reference
The available databases include:
kraken_db: A general-purpose database containing a broad range of microbial genomes for taxonomic classification.kraken2_human_db: A specialized database designed to classify human-associated microbiomes, containing genomes relevant to human health.kraken2_bacteria_db: A targeted database focusing specifically on bacterial genomes, useful for detailed bacterial community analysis.