Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features

作者：Qianhui Zhu, Shenghan Gao, Binghan Xiao, Zilong He, Songnian Hu · 发表于：Microbiology Spectrum · 年份：2023 · DOI：10.1128/spectrum.04645-22 · 被引用次数：56 · 研究领域：Genomics and Phylogenetic Studies、Probiotics and Fermented Foods、Plant Pathogenic Bacteria Studies

assemblies; (ii) applicability for contigs above 500 bp with highest accuracy, enabling plasmid prediction in fragmented short-read assemblies; (iii) excellent and balanced performance between sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which eliminated the bias on sensitivity or specificity that commonly existed in other methods; and (iv) no dependency of species-specific training models. We believe that Plasmer provides a more reliable alternative for plasmid prediction in bacterial genome assemblies.