We also used local realignment to generate candidate alternative haplotypes in the process of calling short (1-50 bp) indels18, as well as local de novo assembly to resolve breakpoints for deletions greater than 50 bp. The latter resulted in a doubling of the number of large (> 1 kb) SVs delineated with base pair resolution19. Full genome de novo assembly was also performed (Supplementary Information), resulting in the identification of 3.7 Mb of novel sequence not matching the reference at a high threshold for assembly quality and novelty. All novel sequence matched other human and great ape sequences in the public databases.
