Centrifuge¶
Description¶
[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. 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 (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers * CENTRIFUGE_INDEXES - indexes directory
Environment Modules¶
Run module spider centrifuge to find out what environment modules are available for this application.
Environment Variables¶
- HPC_CENTRIFUGE_DIR - installation directory
- HPC_CENTRIFUGE_BIN - executable directory
- HPC_CENTRIFUGE_DOC - documentation directory
Categories¶
biology, phylogenetics