Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. 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.
- Version: 1.0.4
- Added: February, 2022
See which versions of centrifuge are available:
$ module avail centrifuge
Load one version into your environment and run it:
$ module load centrifuge/1.0.4 $ centrifuge -h
Note: Please use the ''-p'' option to tell centrifuge how many CPUs/threads it should use for parallel search. This number should match the number of CPUs you requested in your SLURM batch allocation.
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v1.0.4.tar.gz $ tar xf v1.0.4.tar.gz $ cd centrifuge-1.0.4 $ make $ sudo mkdir -p /export/apps/centrifuge/1.0.4 $ sudo chown aorth /export/apps/centrifuge/1.0.4 $ make install prefix=/export/apps/centrifuge/1.0.4 $ sudo chown -R root:root /export/apps/centrifuge/1.0.4
Install extra databases:
$ wget https://zenodo.org/record/3732127/files/h+p+v+c.tar.gz?download=1 -O h+p+v+c.tar.gz $ tar xf h+p+v+c.tar.gz $ sudo cp -v hpvc.* /export/apps/centrifuge/1.0.4/share/centrifuge/indices