Alexander Payne from the University of Nottingham in the UK presented at the 2021 Nanopore Community Meeting about “Barcode-specific adaptive sampling – from human gene panels to viral amplicons.” They spoke about ReadFish or “Read Until” which is an adaptive sampling toolkit. They ran an experiment with four different species to test adaptive sampling for barcodes. Payne explained that they wanted to switch on and off different barcodes. With the same libraries, they were able to target different regions of the sequence. Payne also described another experiment they did with barcode aware adaptive sampling. For 18 Gb of data with a target N50 of 6.997kb, they were still able to confirm fusion events and variants. Payne and team developed a real-time viral sequencing system called MinoTour. The standard ARTIC SARS CoV-2 amplicons are too short for adaptive sampling. With MinoTour and adaptive sampling, amplicon “balancing” leads to more uniform coverage. The use of this approach increased coverage and recovery of complete viral genomes. Multiple applications for adaptive sampling have been enabled with ReadFish and MinKNOW. Payne also hinted at SwordFish, a tool for dynamic experiment updates. Adaptive sampling is available in MinKNOW, and I am excited to use it. I have also been thinking about ways of using adaptive sampling to search for specific sequences, for example.
