#28 · Genomics

Allele reconstruction from Nanopore amplicon reads without target input

The dominant thread is computational inference of allelic and haplotype structure from sequence data, with the two preprints addressing different levels of resolution. A de novo, sequence-first algorithm reconstructs alleles from Oxford Nanopore amplicon reads without requiring target input, and is validated on 20 Coriell CYP2D6 samples. TBLUP, a local DNA tree-based method, estimates haplotype and mutation effects and is shown on simulated and cattle mtDNA data. The new elements are target-free allele reconstruction from long reads and tree-based local modeling of haplotype effects. The UK Biobank whole-genome study of 347,630 individuals is a population-scale heritability analysis and is included here as a separate published reference point rather than a method of the same class. The items do not establish a shared benchmark or ground-truth framework across methods.