Centrifuge+: improving metagenomic analysis upon Centrifuge

SummaryAccurate 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 implementationThe source code is available at https://github.com/mNGSmethods/Centrifugep. Contacth.guo@foxmail.com or jlsljf0101@126.com Supplementary informationSupplementary data are available at Bioinformatics online.