Centrifuge

Centrifuge is a microbial classification engine designed for rapid and accurate identification of species in metagenomic sequencing data on desktop computers. It uses a Burrows-Wheeler transform and Ferragina-Manzini index to create a small index optimized for metagenomic classification, enabling quick classification of millions of reads. Centrifuge has a small index size and can index the entire NCBI nucleotide sequence database, making it useful for large data sets.

Topic

Metagenomics;Microbiology

Detail

  • Operation: Nucleic acid sequence analysis

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.0.4-beta

  • Credit: The National Institutes of Health (NIH), the US Army Research Office, the National Science Foundation (NSF).

  • Input: -

  • Output: -

  • Contact: centrifuge.metagenomics@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • Centrifuge: rapid and sensitive classification of metagenomic sequences.
  • Kim D, et al. Centrifuge: rapid and sensitive classification of metagenomic sequences. Centrifuge: rapid and sensitive classification of metagenomic sequences. 2016; 26:1721-1729. doi: 10.1101/gr.210641.116
  • https://doi.org/10.1101/gr.210641.116
  • PMID: 27852649
  • PMC: PMC5131823

Download and documentation

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