Kaiju

Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from microbial and viral genomes.

Profile Format

Taxpasta expects a five column output. This is generated by the kaiju2table companion tool included with the Kaiju. The following format is expected:

Column Header	Description
file
percent
reads1
taxon_id
taxon_name

Example

file    percent reads   taxon_id    taxon_name
barcode41_se-barcode41-kaiju.tsv    2.988734    841 28901   taxonid:28901
barcode41_se-barcode41-kaiju.tsv    2.739969    771 1902245 taxonid:1902245
barcode41_se-barcode41-kaiju.tsv    2.057642    579 2760310 taxonid:2760310
barcode41_se-barcode41-kaiju.tsv    1.929706    543 1108    taxonid:1108

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1. Value used in standardised profile output ↩