Fig. 7.

The procedure of chimeric read identification and read splicing. To remove the chimeric reads, we first aligned the multiplex PCR primer to the Nanopore sequencing reads and split the reads into segments according to the aligning results. Then, we aligned the read segments to the SARS-CoV-2 genome and discarded those segments that could not be aligned to the reference genome. Finally, we removed the original reads and kept the genome-aligned segments.