Centrifuge - A Low RAM Metagenomic Classifier from Salzberg Group

Apart from metagenome classifiers like NBC and LMAT published in 2011-2013, our readers came across a number of newly published metagenomic classifiers in recent months. Those include Kraken, Clark, Kallisto and the very recent Kaiju from Anders Krogh’s group. They may like another one that is being actively developed (h/t: @StevenSalzberg1). From its github page -

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., 2.9 GB for ~2,800 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.

The novelty of this work is in coming up with a BTW scheme that compresses the microbial genomes within a low memory footprint. You can learn more here.


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Written by M. //