High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
The authors report on a high quality genome assembly of the model plant species Arabidopsis include two telomere-to-telomere assemblies (Chr 3 and 5). PacBio’s HiFi, Oxford Nanopore ultra-long reads and Hi-C (Illumina) were used.
BluePippin was used to size select large fragments from genomic extracts and for Hi-FI library construction. The SageHLS was used to collect DNA fragments >50kb for Oxford Nanopore ultra-long library prep (Genome Center of Grandomics [Wuhan, China]). .
Xi’an Jiaotong University, Xi’an, China
Genomics, Proteomics & Bioinformatics
High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
Ashley Jones ,Cynthia Torkel,David Stanley,Jamila Nasim,Justin Borevitz,Benjamin Schwessinger
The authors provide a protocol for preparing high molecular weight DNA sequencing libraries with a particular focus on difficult plant and fungal tissues, and also can be used with animals and microbes. The libraries can be used for PacBio or Oxford Nanopore sequencing, includes clean up and size selection recommendations, in a manner that is economical and scalable.
The PippinHT was used for the DNA size selection recommendations.
Australian National University, Canberra, Australian Capital Territory, Australia
Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes
Eric S Tvedte, Mark Gasser, Benjamin C Sparklin, Jane Michalski, Carl E Hjelmen, J Spencer Johnston, Xuechu Zhao, Robin Bromley, Luke J Tallon, Lisa Sadzewicz, David A Rasko, Julie C Dunning Hotopp
This side-by-side comparison of PacBio and Oxford Nanopore sequencing platforms for the analysis of E.coli and Drosophila assemblies. The authors provide useful guidance for which platform or approach is better suited for different areas of study, as each platform can provide certain advantages. PacBio’s Sequel II CLR, Sequel II HiFi, and RS II were evaluated as was Oxford Nanopore’s Rapid Sequencing and Ligation Sequencing. Hybrid approaches using Illumina sequencing were also evaluated.
BluePippin was used to size select libraries for both platforms.
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
Department of Biology, Texas A&M University, College Station, TX
Department of Entomology, Texas A&M University, College Station, TX
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
Multiple authors, the SEQC2 Oncopanel Sequencing Working Group
A multi-site and cross-platform evaluation of circulating tumor DNA (ctDNA) NGS assays was conducted by the SEQC2 Oncopanel Sequencing Working Group and reported on in this comprehensive study. Five assays were tested for accuracy, sensitivity and reproducibility including simulations with spike-in DNA. This study is intended to report the state-of-the-art of these assays and inform best practices.
Pippin Prep was used to size select the ctDNA reference samples using 110 bp start and 190 bp end settings for an average fragment length of ~150 bp.
Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
Samuel Martin, Darren Heavens, Yuxuan Lan, Samuel Horsfield, Matthew D Clark, Richard M Leggett
Oxford Nanopore adaptive sampling is a real-time sequencing method with which analysis software identifies several hundred sequence bases as they pass through a pore and decides whether to continue sequencing. If not, the pore voltage is reversed and the associated DNA molecule is ejected. The authors suggest using this method to detect rare or non-abundant species in metagenomic studies of microbial communities. To this end, they created a synthetic mock microbial consortium with seven species, presented different proportions, and tested the method. The authors demonstrate the benefit of this approach and provide a mathematical model to test the suitability for adaptive sampling for environmental metagenomic studies.
BluePippin was used to High-Pass to size select (>15kb) the DNA from the microbial samples prior to Oxford Nanopore library construction.
Earlham Institute, Norwich, UK
Natural History Museum, London