Miten Jain from Northeastern University presented at London Calling 2023 about “A complete analysis of human genomes and transcriptomes using nanopore sequencing.” They spoke about R10.4.1 ultralong DNA sequencing. Jain’s group has been using this sample prep and flow cells with N50s between 90-110 kb and throughput of >100 Gb per PromethION flow cell. The high-accuracy allows for variant calling. Jain and Shafin along with Google Health DeepVariant have developed and tested state-of-the-art SNV calling with R10.4.1 + kit 14. The F1-score is for SNVs with HG002 is 0.99 while indels is 0.88. Jain has also been working with R10.4.1 duplex. They noted that with a PromethION experiment >60% of reads are duplex pairs and accuracy has improved. With duplex, SNV and indel calling is even better. Recently, the RNA 004 kit became available. We have been using the previous RNA002 for bacterial transcriptomics. The improvements in accuracy that Jain described are exciting. They are getting 4-8 M reads with 100 ng of poly(A) RNA and N50s between 1.3-1.5 kb. With the new kit, they can sequence human ribosomal RNA too. Human tRNA can also be sequenced, and Jain shared that they have sequenced all three simultaneously on a PromethION flow cell with reasonable inputs and outputs. The quality of transcriptomes has improved considerably comparing 2019 and 2023 mitochondrial transcript experiments. I would love to try Duplex R10.4.1 experiments and the new direct RNA sequencing kit for genome assembly and transcriptomics.
