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