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. Author manuscript; available in PMC: 2024 Jul 4.
Published in final edited form as: Nat Methods. 2023 Sep 14;20(10):1483–1492. doi: 10.1038/s41592-023-01993-x

Extended Data Fig. 1. Variant calling and methylation analysis using Napu.

Extended Data Fig. 1

Raw ONT sequencing reads are basecalled by Guppy 6.1.2, which simultaneously produces methylation tags. A diploid, de-novo phased assembly is produced using a combination of Shasta and Hapdup. These assemblies are used to call SVs with Hapdiff. Small variants are called against a reference genome with Pepper-Margin-DeepVariant. The phased alignment file generated by Margin is used to produce haplotype-resolved methylation calls. Small variants and SVs are jointly phased by Margin, producing a single harmonized vcf.