Tonight I watched the Oxford Nanopore Technologies (ONT) PAG Industry Workshop session titled “A single-platform solution for plant de novo genome assembly.” Jeannie Mounger, a field applications scientist with ONT, was the presenter. They noted that for plant genome assembly there are several considerations. Plant genome size varies greatly: from Mb to Gb. Polyploidy varies […]
Tonight I continued watching the LISA workshop videos. Lauren Lui from Laurence Berkley National Lab explained the apps available on KBase for long-read only and hybrid assemblies. Using a KBase narrative, Lui shared a Spades short-read-only assembly with 30~ contigs. They described the N50 as a metric for comparing genome assemblies. To calculate N50, contigs […]
I continue to watch the YouTube “Assembly” playlist from the Oxford Nanopore Technologies (ONT) channel. Tonight, I watched session #8! Ian Henderson from the University of Cambridge in the UK presented at the Nanopore Community Meeting 2021. The session was titled “Assembling the centromeres – the ‘black holes’ of the genome.” Henderson said the centromeres […]
Issa Diop from the University of Zurich in Switzerland presented at London Calling 2021 on “Chromosomal-scale assembly of the liverwort Marchantia paleacea.” Diop discussed chloroplasts and endosymbionts before introducing Marchantia as a model of plant evolution. Marchantia has a haploid-dominant life cycle with a genome size of 280 Mbp. There are eight autosomes and 1 […]
Ryan Wick from the University of Melbourne spoke at the Nanopore Community Meeting 2017. They explained that assemblies still fail. The title of the session is “Assembly is still hard: challenges in genome assembly in the era of long reads.” Wick shared an example of a bacterial genome sequence that leads to inaccuracy in sequencing. […]
Tonight I watched Dan Fordham, Director of Strategic Product Management EMEA at Oxford Nanopore Technologies (ONT) speak at London Calling 2023 about. Fordham is the lead for the Org.one project in which ONT tries to address the global biodiversity crisis. ORG.one offers free consumables and kits to users sequencing critically endangered organisms. One of the […]
Dilrini De Silva is a Field Applications Scientist in Bioinformatics for the EMEAI Region with Oxford Nanopore Technologies. De Silva presented a Masterclass at London Calling 2023 entitled “How to take your data analysis further.” This Masterclass focused on typical downstream analysis for several applications including genome assembly, variants, methylation, transcriptomics, and metagenome analysis. De […]
Tomas Marques-Bonet from the Institute of Evolutionary Biology in Spain presented at the Nanopore Community Meeting 2021 about “Org.one: a new program to promote sequencing biodiversity.” Tomorrow London Calling 2023 begins and I am continuing to watch previous sessions. Marques-Bonet highlighted how biodiversity is at risk, with more than 37,400 species threatened with extinction. Amphibians […]
Victoria Shabardina from the Institute of Evolutionary Biology (UPF-CSIC) in Spain presented at London Calling 2022 on “Enigmatic genome of Abeoforma whisleri helps our understanding of the origin of animals.” This eleven-minute session has an intriguing title: what is A. whisleri? They spoke about the origin of multicellularity and the closest unicellular relatives. The organisms […]