centrifuge
rapid and memory-efficient system for classification of DNA sequences
Command lineScience
Not tested on a device yet. What that means
Commands in the package
centrifugecentrifuge-buildcentrifuge-compresscentrifuge-downloadcentrifuge-inspect
About centrifuge
From Debian's package description
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.
From Debian's description of the centrifuge package, under that package's license.
Dependencies
Depends on
Related apps
- bowtie2ultrafast memory-efficient short read alignerCommand line
- salmidrapid Kmer based Salmonella identifier from sequence dataCommand line
- bowtieUltrafast memory-efficient short read alignerCommand line
- freefem++Provides the binaries of the FreeFem++ FE suiteCommand line
- wisecomparison of biopolymers, like DNA and protein sequencesCommand line
- hhsuitesensitive protein sequence searching based on HMM-HMM alignmentCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the centrifuge package, under that package's license.
- Description: Debian's description of the centrifuge package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.