Fig. 2.

Structural variants in lung cancers identified by PromethION. a Five representative types of structural variants in cancer genomes. Ref.: Reference sequences. b The workflow of direct, long-read whole-genome sequencing analysis by PromethION [10]. Intact high-molecular-weight genomic DNA is extracted from fresh or frozen cells. For the construction of sequencing libraries of PromethION, DNA repair, end-prep, and adaptor ligations are conducted according to the manufacturer’s protocols. Sequencing starts after the library is loaded to the flow cell. Base calling is performed to obtain the sequencing read data, because the data are first provided in the fast5 file format. After getting the fastq files, the reads are mapped to the reference genome and/or assembled, and various analyses are conducted, such as SNV/SV calling, methylated base calling, phasing analysis, and visualization by genome viewers