What it does

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise.

Output Format

Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are:

1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified.
2. The sequence ID, obtained from the FASTA/FASTQ header.
3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified.
4. The length of the sequence in bp.
5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that:
        a) the first 13 k-mers mapped to taxonomy ID #562
        b) the next 4 k-mers mapped to taxonomy ID #561
        c) the next 31 k-mers contained an ambiguous nucleotide
        d) the next k-mer was not in the database
        e) the last 3 k-mers mapped to taxonomy ID #562