Barcode-specific adaptive sampling — from human gene panels to viral amplicons
About Alexander Payne
Alex is a Ph.D. student at the University of Nottingham working with Matt Loose. After studying biology, Alex became interested in genomics and bioinformatics. During his Ph.D. his focus has been on developing ReadFish, a selective sequencing method for nanopore devices. ReadFish analyses molecules as they are being sequenced, either accepting or rejecting the in-progress reads. In addition to real-time analysis, Alex is the author of BulkVis — a tool for finding ultra-long reads in nanopore datasets.
The ability to selectively sequence individual molecules of DNA from a sequencing library is a unique property of Oxford Nanopore sequencers. A key practical application of this technology is processing multiple samples on a single flow cell, where each sample is identified by a unique barcode. Here, we extend our adaptive sampling tool, ReadFish, to become 'barcode-aware', enabling users to select different targets within each barcoded sample or to filter out individual barcodes from a sample. We have used this approach to target gene panels and individual amplicons for specific barcodes; and to 'switch off' entire barcodes once sufficient data have been generated.