File: kaiju.md

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---
name: Kaiju
url: http://kaiju.binf.ku.dk/
description: Fast and sensitive taxonomic classification for metagenomics
---

The Kaiju module parses output generated by kaiju2table from [Kaiju](http://kaiju.binf.ku.dk/),
a fast and sensitive taxonomic classification for metagenomics.
e.g:

```bash
kaiju -i R1.fq.gz -j R2.fq.gz -o output_kaiju.txt
kaiju2table -t nodes.dmp -n names.dmp -r species -o kaiju2table_species.txt output_kaiju.txt
kaiju2table -t nodes.dmp -n names.dmp -r phylum -o kaiju2table_phylum.txt output_kaiju.txt
```