What a busy day! We tried VolTRAX and Miro library preps today as part of the PORES workshop. We also did DNA extractions, a Miroculus workshop, and lots of moving around. Tonight I watched the London Calling 2023 session entitled “MethPhaser: automated methylation-based haplotype phasing of human genomes with Oxford Nanopore sequencing” with Fritz Sedlazeck from Baylor College of Medicine & Rice University. They spoke about the TPMT gene that encodes an enzyme that metabolizes thiopurine drugs and how phasing really matters in scenarios such as this. Sedlazeck noted that long-reads are powerful for phasing but there are limitations. They tested different flow cells and coverage of the human genome HG002 and MethPhaser. This software requires phased SNV and BAM file. They tested MethPhaser and the errors made. MethPhaser improved N50 of patient samples and help reduce the number of phaseblocks. They concluded that MethPhaser is “the first method that combines long-read epigenomic and genomic variant for genome scale phasing” and “achieves 1.5-3X phaseblock N50 length against SNV-based methods on human samples.” I thought it was interesting that MethPhaser “rescued previously un-tagged reads” thus improving SNV-based approaches.
