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  • Description

    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.

  • Usage

    To list all executables provided by Centrifuge, run: $ biogrids-list centrifuge Copy to clipboard
  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install centrifuge Copy to clipboard Available operating systems: Linux 64, OS X INTEL
  • Primary Citation*

    D. Kim, L. Song, F. P. Breitwieser, and S. SL.. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26(12): 1721-1729.

    • *Full citation information available through