Kaiju

Introduction

Kaiju is a tool for fast taxonomic classification of metagenomic sequencing reads using a protein reference database.

For more information, please check its website: https://biocontainers.pro/tools/kaiju and its home page on Github.

Versions

• 1.8.2

Commands

• kaiju

• kaiju-addTaxonNames

• kaiju-convertMAR.py

• kaiju-convertNR

• kaiju-excluded-accessions.txt

• kaiju-gbk2faa.pl

• kaiju-makedb

• kaiju-mergeOutputs

• kaiju-mkbwt

• kaiju-mkfmi

• kaiju-multi

• kaiju-taxonlistEuk.tsv

• kaiju2krona

• kaiju2table

• kaijup

• kaijux

Module

You can load the modules by:

module load biocontainers
module load kaiju

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Kaiju on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=kaiju
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers kaiju

kaiju -t kaijudb/nodes.dmp \
     -f kaijudb/refseq/kaiju_db_refseq.fmi \
    -i input_1.fastq -j input_2.fastq
     -z 24