kaiju
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'kaiju' Versions
- 1.8.2
Link to section 'Commands' of 'kaiju' 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
Link to section 'Module' of 'kaiju' Module
You can load the modules by:
module load biocontainers
module load kaiju
Link to section 'Example job' of 'kaiju' Example job
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