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. Centrifuge requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial genomes) yet provides very fast classification speed, allowing it to process a typical DNA sequencing run within an hour. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. 




To see what versions of Centrifuge are available type

module avail centrifuge

To see what other modules are needed, what commands are available and how to get additional help type

module help  centrifuge

To use Centrifuge, include a command like this in your batch script or your interactive session to load the Centrifuge module:

module load centrifuge


Be sure you also load any other modules needed, as listed by the module help centrifuge command.




User Information

Connect to PSC systems:
Technical questions:

Send mail to remarks@psc.edu or call the PSC hotline: 412-268-6350.