Extended Data Figure 2. Variant detection pipeline.

At every variant locus, we collected the full-length reads that overlap the locus, performed de novo assembly using the Celera assembler, and called a consensus using Quiver after remapping reads used in the assembly as well as reads flanking the assembly (yellow reads) to increase consensus quality at the boundaries of the assembly. BLASR is used to align the assembly consensus sequences to the reference, and insertions and deletions in the alignments are output as variants. Reads spanning a deletion event within a single alignment are shown as bars connected by a solid line, and double hard-stop reads spanning a larger deletion event and split into two separate alignments of the same read are shown as a dotted line.