Tag Archives: BluePippin

Optimising ddRAD sequencing for population genomic studies with ddgRADer

October 2022 Authors: Aparna Lajmi, Felix Glinka, Eyal Privman Info: In this preprint, the authors describe an online webtool that they have developed for designing ddRAD-seq experiments. This webtool assists in the recommendation of restriction enzyme pairs and size-selection criteria. … more »

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Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients

September 2022 Authors: Elsie Cheruba, Ramya Viswanathan, Pui-Mun Wong, Howard John Womersley, Shuting Han, Brenda Tay, Yiting Lau, Anna Gan, Polly S. Y. Poon, Anders Skanderup, Sarah B. Ng, Aik Yong Chok, Dawn Qingqing Chong, Iain Beehuat Tan, Lih Feng … more »

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An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing

Feb 2022 Authors: Catherine D. Aimone, Steen Hoyer, Anna E. Dye, David O. Deppong, Siobain Duffy, Ignazio Carbone, Linda Hanley-Bowdoin Info: The authors provide a protocol for analyzing single stranded DNA (ssDNA) from begomoviruses, which cause significant damage to many … more »

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High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

September 2021 Authors: Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye Info: The authors report on a high quality genome assembly of the model … more »

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Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

June 2021 Authors: 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 Info: This side-by-side comparison of … more »

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Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

May 2021 Authors: Samuel Martin, Darren Heavens, Yuxuan Lan, Samuel Horsfield, Matthew D Clark, Richard M Leggett Info: Oxford Nanopore adaptive sampling is a real-time sequencing method with which analysis software identifies several hundred sequence bases as they pass through … more »

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Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

Authors: Arthur Demené , Benoît Laurent , Sandrine Cros-Arteil , Christophe Boury , Cyril Dutech Info: The authors present a high-quality de novo genome assembly of Cryphonectria parasitica, and invasive fungus that causes chestnut blight, using Oxford Nanopore and Illumina … more »

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isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

January 2021 Authors: Ruijiao Xin, Yan Gao, Yuan Gao, Robert Wang, Kathryn E. Kadash-Edmondson, Bo Liu, Yadong Wang, Lan Lin & Yi Xing Info: The authors present a protocol, isoCirc, for the full-length sequence determination of circular RNAs. The method … more »

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A long-read RNA-seq approach to identify novel transcripts of very large genes

July 2020 Authors: Prech Uapinyoying, Jeremy Goecks, Susan M. Knoblach, Karuna Panchapakesan, Carsten G. Bonnemann, Terence A. Partridge, Jyoti K. Jaiswal, and Eric P. Hoffman Info: Scientists researching muscular disorders present a method for studying gene expression of large RNA … more »

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Fully phased sequence of a diploid human genome determined de novo from the DNA of a single individual

July 2020 Authors: Ilya Soifer , Nicole L. Fong, Nelda Yi, Andrea T. Ireland, Irene Lam, Matthew Sooknah, Jonathan S. Paw, Paul Peluso, Gregory T. Concepcion, David Rank, Alex R. Hastie, 5 Vladimir Jojic, J. Graham Ruby, David Botstein, Margaret … more »

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