centrifuge-compress
rapid and memory-efficient system for classification of DNA sequences
Install
- All systems
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curl cmd.cat/centrifuge-compress.sh
- Debian
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apt-get install centrifuge - Ubuntu
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apt-get install centrifuge - Kali Linux
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apt-get install centrifuge - Windows (WSL2)
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sudo apt-get updatesudo 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.