centrifuge-compress

rapid and memory-efficient system for classification of DNA sequences

Install

All systems
curl cmd.cat/centrifuge-compress.sh
Debian Debian
apt-get install centrifuge
Ubuntu
apt-get install centrifuge
image/svg+xml Kali Linux
apt-get install centrifuge
Windows (WSL2)
sudo apt-get update sudo apt-get install centrifuge
Dockerfile
dockerfile.run/centrifuge-compress

centrifuge

rapid and memory-efficient system for classification of DNA sequences

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.