Okamoto, F. (BMEB) – Improving read-to-pangenome alignment in complicated genomic regions

Many genetics pipelines start by aligning sequencing reads to a reference genome. Aligners attempt to find the position in the reference sequence which best matches the read sequence, but this breaks down when the reads come from a sample with variation relative to the reference. A proposed alternative, pangenome graphs, is supposed to fix such “reference bias” by including known variation within the reference itself. Yet read alignment is still difficult in graph regions featuring certain complex variation. I will address specific known limitations of pangenome read alignment by developing better methods to align reads to pangenomes (1) in centromeres, (2) in regions with cycles, (3) when a “split”/supplementary alignment is required, and (4) for RNA-seq reads.

Event Host: Faith Okamoto, Ph.D. Student, Biomolecular Engineering & Bioinformatics

Advisor: Benedict Paten

Zoom: https://ucsc.zoom.us/j/3543092299?pwd=5xbPfPhxvoJlx24tusiOwPuLSjzwzb.1

Passcode: 767376