====== centrifuge ======

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.

===== Information =====

  * Version: 1.0.4
  * Added: February, 2022
  * Link: https://ccb.jhu.edu/software/centrifuge/

===== Usage =====

See which versions of centrifuge are available:
<code>$ module avail centrifuge</code>

Load one version into your environment and run it:
<code>$ module load centrifuge/1.0.4
$ centrifuge -h</code>

**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.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>

Install extra databases:

<code>$ 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</code>