Bio Long Read Sequencing Long Read Alignment

Aligns Oxford Nanopore and PacBio long reads (and assemblies) to a reference with minimap2 using the error-rate-matched preset (map-ont, lr:hq, map-hifi, map-pb, splice/splice:hq, asm5/10/20, ava), producing a sorted/indexed BAM for variant, SV, methylation, or isoform analysis. Covers why the preset rewrites the scoring/chaining model, why SV calling rides on supplementary not secondary alignments, carrying MM/ML methylation tags through with -y, the multi-part-index MAPQ trap, and when to swap in Winnowmap/VACmap/lra/pbmm2. Use when mapping ONT or PacBio reads, choosing a minimap2 preset by platform/chemistry, preparing input for Clair3/medaka/Sniffles/modkit, aligning …