Fig. 2

A. IGV viewer alignment on the PML and RARA genes of a Flongle Nanopore generated sequences for the NB4 cell line. Library was generated from DNA with a PCR-free enrichment protocol using CRISPR guides targeting PML and RARA genes. The top panel shows the alignment for the reads processed with the Bonito basecaller and minimap2 aligner in the Bwb. The middle panel shows the alignment of reads processed with the Guppy basecaller and minimap2 aligner in the Bwb workflow. The bottom panel shows reads processed in a manual step-by-step workflow using the Guppy flipflop basecaller and minimap2 aligner. Reads with PML-RARA breakpoint are colored to highlight the fragment aligned to PML and RARA.B. Genomic BCR-ABL1 breakpoint identified in the K562 cell line by long-read sequencing. Schematic representation (generated with http://wormweb.org/exonintron) shows the breakpoint captured with our amplification-free enrichment protocol and long-read sequencing. The breakpoint is represented in the upper graphic by the red vertical line, and the location of the sequence specific guides is marked by colored arrows. ABL1 intron 1 spans 140Kbs. In the lower panel, nanopore sequence alignments in IGV show sequences partially aligned to BCR and ABL1. Reads with BCR-ABL1 breakpoint are colored to highlight the same read is partially aligned to BCR and ABL1.