Centrifuge: rapid and sensitive classification of metagenomic sequences
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Abstract
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 an 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 (4.2 GB for 4078 bacterial and 200 archaeal genomes) 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. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k -mer-based indexing schemes, which require far more extensive space.
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Customized bioinformatics pipelines for clinical mNGS data still require highly trained programming staff to develop, validate and maintain for clinical use.
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From Clinical metagenomics (2019) · cites this paper as [110]
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- Authors
- Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L.
- Affiliations
- Johns Hopkins University (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2016-10-17
- Volume
- 26
- Issue
- 12
- Pages
- 1721-1729
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC5131823
- OpenAlex
- W2951160681
- Cited by
- 1,438
- References
- 32
- Citations by year
- 2026: 128 · 2025: 175 · 2024: 209 · 2023: 174 · 2022: 170 · 2021: 184 · 2020: 178 · 2019: 108 · 2018: 71 · 2017: 36 · 2016: 4 · 2013: 1
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health (R01-HG006677, R01-GM083873, W911NF-1410490)
- National Science Foundation (ABI-1356078)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- centrifuge, metagenomic sequence classification, microbial taxonomy, Burrows-Wheeler transform, FM-index, sequence indexing, bacterial genomes, archaeal genomes, desktop computing
- MeSH terms
- Algorithms, Archaea, Bacteria, Sequence Analysis, DNA, Computational Biology, Databases, Nucleic Acid, Metagenomics, High-Throughput Nucleotide Sequencing
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