Abstract
Summary Accurate abundance estimation of species is essential for metagenomic analysis. Although many methods have been developed for classification of metagenomic data and abundance estimation of species, the abundance estimation of species remains challenging due to the ambiguous reads that align equally well to more than one genome. Here, we present Centrifuge+, which introduces unique mapping rate to describe the influence of similarities among species in the reference database when analyzing ambiguous reads. In contrast to the popular Centrifuge, Centrifuge+ improved the accuracy of abundance estimation on simulated reads from 4278 complete prokaryotic genomes.
Availability and implementation The source code is available at https://github.com/mNGSmethods/Centrifugep.
Contact h.guo{at}foxmail.com or jlsljf0101{at}126.com
Supplementary information Supplementary data are available at Bioinformatics online.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
↵† The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.