Applications/Centrifuge
Application Details
- Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species.
- Version: 1.0.4 (and 1.0.4a see text below)
- Modules: centrifuge/1.0.4 and centrifuge/1.0.4a
- Licence: Open source (Github)
Usage Examples
[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labelling 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 a 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 (1.0.4) is the main GitHub repo with 1.0.4a as the patched version according to
- https://github.com/DaehwanKimLab/centrifuge/commit/a5c09bb29a3a828d88be49c55353cd84b6b9bbad
- https://github.com/DaehwanKimLab/centrifuge/commit/4f2877ca7620d556afd0eff1bee5bfc224b31b7c
[username@login01 ~]$ module add centrifuge/1.0.4 or [username@login01 ~]$ module add centrifuge/1.0.4a