Centrifuge

Introduction

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers.

For more information, please check its website: https://biocontainers.pro/tools/centrifuge and its home page: http://www.ccb.jhu.edu/software/centrifuge/.

Versions

  • 1.0.4_beta

Commands

  • centrifuge

  • centrifuge-BuildSharedSequence.pl

  • centrifuge-RemoveEmptySequence.pl

  • centrifuge-RemoveN.pl

  • centrifuge-build

  • centrifuge-build-bin

  • centrifuge-class

  • centrifuge-compress.pl

  • centrifuge-download

  • centrifuge-inspect

  • centrifuge-inspect-bin

  • centrifuge-kreport

  • centrifuge-sort-nt.pl

  • centrifuge_evaluate.py

  • centrifuge_simulate_reads.py

Module

You can load the modules by:

module load biocontainers
module load centrifuge

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 Centrifuge on our clusters:

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

module --force purge
ml biocontainers centrifuge

centrifuge-download -o taxonomy taxonomy
centrifuge-download -o library -m -d "archaea,bacteria,viral" refseq > seqid2taxid.map
cat library/*/*.fna > input-sequences.fna
centrifuge-build -p 8 --conversion-table seqid2taxid.map \
             --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp \
             input-sequences.fna abv