ArticleGenome biology2024
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Optimizing protocols for microRNA profiling of infant and toddler stool.RNA biology · 2026Article
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- TDKC (Target Distilled K-mer Classifier): Ultrafast and Memory-Efficient Sequence Classification for Target Pathogen Diagnostics.bioRxiv : the preprint server for biology · 2026Article
- Urban green roofs host intrinsic resistomes shaped by management but not dominated by pathogenic resistance.BMC microbiology · 2026Article
- Pharmacokinetics of Long-Acting Ampicillin and Its Impact on the Gut Microbiome and Resistome in Rhesus Macaques (Macaca mulatta).Journal of veterinary pharmacology and therapeutics · 2026Article
- Bacterial Community Composition and Functional Potential of the Kleptoplastic Sea SlugBiomolecules · 2026Article
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- Kun-peng enables scalable and accurate pan-domain metagenomic classification.Briefings in bioinformatics · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- MMonitor for real-time monitoring of microbial communities using long reads.Cell reports methods · 2026Article
- Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026Article
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.Frontiers in bioinformatics · 2026Article
- Article
- Engineering rank queries on bit vectors and strings.Algorithms for molecular biology : AMB · 2025Article
- Robust 16S rRNA classification based on a compressed LCA index.Genome research · 2025Article
- Expansion of the plant-parasitic nematode RNA viruses: Unprecedented diversity, intron-bearing viruses, and cross-kingdom evolutionary links.NPJ biofilms and microbiomes · 2025Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.Communications biology · 2025Article
Corrections and comments
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2 authors.
Funding
Abstract
Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the Burrows-Wheeler transformed genome sequences are losslessly compressed using a novel scheme called run-block compression. Run-block compression achieves sublinear space complexity and is effective at compressing diverse microbial databases like RefSeq while supporting fast rank queries. Combining this compression method with other strategies for compacting the Ferragina-Manzini (FM) index, Centrifuger reduces the memory footprint by half compared to other FM-index-based approaches. Furthermore, the lossless compression and the unconstrained match length help Centrifuger achieve greater accuracy than competing methods at lower taxonomic levels.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.