A dual-process of targeted and unbiased Nanopore sequencing enables accurate and rapid diagnosis of lower respiratory infections.

"metagenomic sequencing data with human genome removed were deposited as national center for biotechnology information (ncbi) sequence read archive (sra) under bioproject prjna818777."

"Declaration of interests Yifan Guo, Lijuan Li, Lingxiao Sun, Yuyao Yin, Shijun Sun, Binghuai Lu, Jiajing Han, Kang Chang, Li Gu, Chendi Jing, Hongbin Chen, and Hui Wang declare that they have no conflict of interest. Zhenzhong Li, Shan Li, Xinfang Yang, Yan Dai, Ju Gu, Lan Yang, Xue Liu, Manjiao Liu, Hui Xu, Ryon Liu, Yong Ren and Hao Guo are affiliated with Simcere Diagnostics Co., Ltd and Nanjing Simcere Medical Laboratory Science Co., Ltd."

"This study was supported by the 10.13039/501100012166National Key Research and Development Program of China (grant number 2018YFE0102100) and 10.13039/501100001809National Natural Science Foundation of China (grant number 81625014)."