Difference between revisions of "Applications/Centrifuge"
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| − | #SBATCH -J | + | #SBATCH -J centrifuge |
| − | #SBATCH -p | + | #SBATCH -p compute |
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#SBATCH -o %N.%j.%a.out | #SBATCH -o %N.%j.%a.out | ||
#SBATCH -e %N.%j.%a.err | #SBATCH -e %N.%j.%a.err | ||
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#SBATCH --exclusive | #SBATCH --exclusive | ||
| − | #SBATCH -t 00: | + | #SBATCH -t 00:10:00 |
module purge | module purge | ||
Latest revision as of 09:50, 17 November 2022
Application Details
- Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species.
- Version: 1.0.4 (and 1.0.4a see text below)
- Modules: centrifuge/1.0.4 and centrifuge/1.0.4a
- Licence: Open source (Github)
Usage Examples
[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome). It classifies sequences at a very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers
- The Centrifuge homepage is http://www.ccb.jhu.edu/software/centrifuge
- The Centrifuge paper is available at https://genome.cshlp.org/content/26/12/1721
centrifuge (1.0.4) is the main GitHub repo with 1.0.4a as the patched version according to
- https://github.com/DaehwanKimLab/centrifuge/commit/a5c09bb29a3a828d88be49c55353cd84b6b9bbad
- https://github.com/DaehwanKimLab/centrifuge/commit/4f2877ca7620d556afd0eff1bee5bfc224b31b7c
[username@login01 ~]$ module add centrifuge/1.0.4 or [username@login01 ~]$ module add centrifuge/1.0.4a
Batch Job
#!/bin/bash #SBATCH -J centrifuge #SBATCH -p compute #SBATCH -o %N.%j.%a.out #SBATCH -e %N.%j.%a.err #SBATCH --exclusive #SBATCH -t 00:10:00 module purge module load centrifuge/1.0.4 ###Run your commands### centrifuge-download -o library -d "vertebrate_mammalian" -a "Chromosome" -t 9606,10090 -c 'reference genome' >> seqid2taxid.map #etc...