NCM 2022: Incorporating ultra-long Oxford Nanopore Technologies reads in VGP high quality reference genome assemblies
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The Vertebrate Genomes Project (VGP) aims to create an open-access genome repository cataloging at least one high-quality, near-gapless, chromosome-level, phased, and annotated reference genome assembly for all ~70,000 extant vertebrate species. Technologies are rapidly developing and in the short time since the formation of the VGP consortium, the pipeline utilizes a combination of long-read and long-range technologies. Our group, the Vertebrate Genome Lab (VGL), is one of the main data production and assembly hubs for the VGP. Samples acquired from an extensive network of collaborators are bio-banked into the collection before undergoing a variety of specialized preparation techniques. These include high molecular weight DNA extraction methods as well as quality control to assess fragment length and appropriate yield in preparation for PacBio sequencing and Bionano optical mapping. PacBio high fidelity (HiFi) sequences are used to create the initial assembly, and then optical maps and Hi-C sequences are used for scaffolding, which increase the contiguity of the assembly (VGP assembly pipeline v2.1). We at VGL are currently optimizing our Oxford Nanopore Technologies (ONT) workflow for a wide variety of non-model organisms that have not been previously sequenced on this platform, from DNA extraction to library preparation and sequencing, aiming to maximize N50, long reads (>100kb), and data output. This necessitates working with an extremely diverse set of samples in terms of taxonomy, tissue type, and quality. As such, it is challenging to formulate one workflow that produces dependable results. We present results from varying extraction methods and library preparation modifications.
