Software: Centrifuge
Description
Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers.
Available Versions
| Unspecified: | 1.0.4_beta |
|---|
For more information, please check its website: https://biocontainers.pro/tools/centrifuge and its home page: http://www.ccb.jhu.edu/software/centrifuge/.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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