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Saturday, February 20, 2021

Case Study: Diving Deep – Revealing the mysteries of marine life with SMRT Sequencing

Many scientists are using PacBio Single Molecule, Real-Time (SMRT) Sequencing to explore the genomes and transcriptomes of a wide variety of marine species and ecosystems. These studies are already adding to our understanding of how marine species adapt and evolve, contributing to conservation efforts, and informing how we can optimize food production through efficient aquaculture.

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Friday, February 5, 2021

SMRT Leiden: Cas9 off-target sequencing and analysis

In this SMRT Leiden 2020 Online Virtual Event presentation, Ida Hoijer of Uppsala University shares her research on developing a long-read sequencing-based method for detection of CRISPR-Cas9 off-target effects, along with a customized analysis pipeline. By applying an off-target sequencing (OTS) method on a human embryonic cell line, they detected 55 on- and off-target sites for three different gRNAs, including allele-specific off-targets. As the OTS approach finds off-targets that are difficult to predict using in silico or short-read based methods, it may become an important tool for genome editing.

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Friday, February 5, 2021

SMRT Leiden: The impact of polishing on Darwin Tree of Life chromosome-level lepidopteran genome assemblies built with PacBio HiFi and Illumina Hi-C reads

In this SMRT Leiden 2020 Online Virtual Event presentation, Marcela Uliano da Silva of Wellcome Sanger Institute shares her work using CCS data combined with HiC reads to assemble chromosome-level genomes for Lepidoptera. This was done as part of the The Darwin Tree of Life Project which is assembling high-quality genomes for all eukaryotic species in Britain and Ireland. Find data: https://github.com/darwintreeoflife/darwintreeoflife.data

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Friday, February 5, 2021

Webinar: Bioinformatics lunch & learn – A quick guide to metagenomic analysis with PacBio HiFi reads

In this webinar, scientists from PacBio share how using Single Molecule, Real-Time (SMRT) Sequencing, you can generate highly accurate long reads – HiFi reads – with 99% accuracy (Q20) and read lengths of 10 kb or more. This high resolution of each single molecule enables species or strain-level profiling of complex populations in both targeted and shotgun sequencing experiments. Genome assemblies are more cost effective than ever before when sequencing metagenomics samples with the Sequel II System.

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Friday, February 5, 2021

SMRT Leiden: Epigenomics in the ERA of third-generation sequencing: A large-scale study of the human pathogen Clostridioides difficile

In this SMRT Leiden 2020 Online Virtual Event presentation Pedro Oliveira of Mount Sinai shares his research on Clostridioides – a leading cause of nosocomial-acquired diarrhea and colitis across the developed world. In this study, Oliveira and coworkers performed the first comprehensive DNA methylome analysis of 36 human C. difficile isolates from a hospital setting using SMRT Sequencing and comparative epigenomics.

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Friday, February 5, 2021

SMRT Leiden: Calling all variants with HiFi reads

In this SMRT Leiden 2020 Online Virtual Event presentation, William Rowell of PacBio shares work on using HiFi reads – which combine the length of traditional long reads with the accuracy of short reads, making them great for comprehensive variant detection. This presentation covers the recommended workflows for detecting both small variants and structural variants from HiFi reads.

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Friday, February 5, 2021

Spanish Language Webinar: Introducción a la secuenciación larga y precisa con PacBio

En este seminario online Carmen Guarco, Senior Field Application Scientist especializada en Bioinformática en PacBio, ofrece una introducción a la tecnología de secuenciación SMRT, las secuencias HiFi y sus aplicaciones incluyendo el ensamblaje de genomas y la secuenciación de ARN. Álvaro G. Hernandez, Director de la Unidad de Secuenciación de ADN en la Universidad de Illinois at Urbana-Champaign, ofrece recomendaciones para asegurar que la secuenciación de genomas sea de alta calidad con ejemplos de parámetros que definen una buena secuenciación. Además, cubre los beneficios de secuenciación del gen 16S en comparación con secuenciación de regiones variables con ejemplos de la…

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Friday, February 5, 2021

SMRT Leiden: The functional iso-transcriptomics pipeline: from long reads to biological insights

In this SMRT Leiden 2020 Online Virtual Event presentation, Ana Conesa of the University of Florida shares her work on the latest updates to the Funciitonal Iso-Annot software, that includes SQANTI, IsoAnnot and tappAS. SQANTI includes new features such as assessment of TSS and TTS sites and sequencing depth. SQANTI3 includes direct annotation of IsoAnnot annotation labels and direct compatibility with tappAS for differential splicing analysis and functional annotation of long reads data.

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