Kraken2

Kraken2 uses k-mers to identify the taxonomy of the microbes in your sample. In essence, they have taken all complete genomes, and then identified all k-mers that are unique to each taxonomic level. Through some nifty computing, and special data structures, they have figured out how to search this very efficiently.

There are a wide range of pre-built kraken databases that you can download, so you do not need to go to the effort of building them yourself.

When installing Kraken2, I recommend setting the KRAKEN2_DB_PATH and KRAKEN2_DEFAULT_DB variables, and then you do not need to specify them on the command line.

To run Kraken2, use this incantation:

kraken2 --paired --threads 4 --report kraken_taxonomy.txt --output kraken_output.txt \
	fastq/reads_1.fastq fastq/reads_2.fastq

This will output two files:

• $SRR.kraken_output.txt contains the standard kraken output:
  • A code (C or U) indicating whether the read was classified or not
  • The read ID from the fastq file
  • The taxonomy ID assigned to the read if it is classified, or 0 if it is not classified
  • The length of the sequence in base pairs. Because we are using paired end reads, there are two lengths (R1|R2)
  • A space-separated list of the lowest common ancestor for each sequence that indicates how many kmers map to which taxonomic IDs. Because we have paired end information, there is a |:| separator between the R1 and R2 information
• $SRR.kraken_taxonomy.txt contains the standard kraken report:
  • Percent of fragments at that taxonomic level
  • Number of fragments at that taxonomic level (the sum of fragments at this level and all those below this level)
  • Number of fragments exactly at that taxonomic level
  • A taxonomic level code: Unclassified, Root, Domain, Kingdom, Phylum, Class, Order, Family, Genus, or Species. If the taxonomy is not one of these the number indicates the levels between this node and the appropriate node. See the docs for more information.
  • NCBI Taxonomic name
  • Scientific name

For more information about Kraken2, see the wiki page

If you are using the HPC at Flinders University, the details on this page will show you how to install and use Kraken2