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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.

Profile Format

A Kraken-style txt output file produced by the centrifuge-kreport auxiliary tool (a part of the Centrifuge package) is accepted by taxpasta.

Column Header Description


  0.00  0   0   U   0   unclassified
100.00  99  0   -   1   root
 98.99  98  0   D   10239     Viruses
 33.33  33  0   F   687329      Anelloviridae
 23.23  23  1   G   687331        Alphatorquevirus
  1.01  1   1   S   687340          Torque teno virus 1
  1.01  1   1   S   687342          Torque teno virus 3

  1. Value used in standardised profile output