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