Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification

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...

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Bibliographic Details
Published inGenome Biology Vol. 25; no. 1; p. 106
Main Authors Song, Li, Langmead, Ben
Format Journal Article
LanguageEnglish
Published England BioMed Central 25.04.2024
BMC
Subjects
Chlamydia
Classification
Compact data structure
Compression
Data Compression - methods
FM-index
genome
Genome, Bacterial
Genome, Microbial
Genomes
memory
Metagenomic
Metagenomics
Metagenomics - methods
r-index
Sequence Analysis, DNA - methods
Software
Taxonomy
FM-index
r-index
Compact data structure
Metagenomic
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Summary: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-024-03244-4