Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
复制标题
离心机：无损压缩微生物基因组，以实现高效、准确的宏基因组序列分类。
DOI：
10.1101/2023.11.15.567129
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Langmead,Ben
中科院分区：
文献类型：
--
作者：
Song,Li;Langmead,Ben
测序仪是一种有效的分类学分类方法，它将测序读数与微生物基因组数据库进行比较。在Burrows-Wheeler中，Burrows-Wheeler转换的基因组序列使用称为运行块压缩的新方案进行有损压缩。运行块压缩实现了次线性空间复杂性，并且在压缩RefSeq等不同微生物数据库时有效，同时支持快速排名查询。将这种压缩方法与其他用于压缩Ferragina-Manzini（FM）索引的策略相结合，与其他基于FM索引的方法相比，Repliger将内存占用减少了一半。此外，无损压缩和不受约束的匹配长度帮助Escherger在较低的分类学水平上实现比竞争方法更高的准确性。
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.