PacBio - Monthly Newsletter (April)

pacbio_shortlogo_color_rgb-01.jpgAlthough the current circumstances mean events are delayed or cancelled, we have many updates for you to explore about how PacBio and the Sequel II is changing the face of long-read sequencing. This month we bring all the latest from high quality genomes, human genomics, webinars to view, a new sample prep method and more!



Webinars

As you tackle the important questions that drive your research, make sure you understand how the power of SMRT Sequencing can help uncover the answers. Explore the recent and upcoming webinars.

Webinars from March:

Upcoming Webinar:

Title: Sequencing the Polyploid Redwood Genome with Highly Accurate Long Reads from PacBio.
Date: Tuesday 14th April, 2020
Time: 1pm (Sydney

Register Now



High Quality Genomes

p1.pngBeyond Contiguity – Assessing the Quality of Genome Assemblies with the 3 C's. How does one properly measure the accuracy of a generated genome assembly? We explored several methods you might find useful and broke them down by what type of orthogonal data is needed for each.
Read the full post

And we would like to add one more C. Compute. Only 6 Days to assemble a 27Gb hexaploid genome! Crazy! At the end of January PacBio decided to see just how far they could push HiFi when it comes to large, complex genomes and embarked on a project to sequence the California redwood. Not surprisingly it worked great! PacBio generated an excellent genome in terms of contiguity, completeness, and correctness, and it was done in just 17 days from sample to assembly. It's written up here in a nice Medium post about the project and results. You can also register for an upcoming webinar on April 14th, 1pm Sydney time, to hear more about how they did this project.

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getimage-1.jpegA Rose is a Rose: HiFi Reads Enable Sequencing of Complex Tetraploid Species. Read about how PacBio HiFi reads are helping Dutch researchers overcome the hurdles of sequencing the rose genome.


p3.pngMeerkats, yaks, geese, and lots of flies -- oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project. The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data. Many were created using PacBio sequencing data. Read the full PacBio blog about this release here.




Bioinformatics of HiFi Reads for Genome Assembly

getimage-2.jpegSince its release in 2019, the bioinformatics community has been developing new tools that take advantage of the highly accurate long reads, known as HiFi reads, for genome assembly and variant calling. Read about the some of the newest tools in these posts by Liz Tseng of PacBio:


HiFi Assembler Series, Part 1: hifiasm, a fast, haplotype-resolved genome assembler
HiFi Assembler Series, Part 2: HiCanu, near optimal repeat resolution using HiFi reads

Listen to this webinar recording to learn how to assemble genomes with HiFi reads using FALCON



Ultra-Low Input Sample Prep

p5.pngCheck out this poster describing a new method for ultra-low DNA input PacBio library prep. A high-quality PacBio insect genome from only 5 ng of input DNA!




Human Genomics

PacBio HiFi reads are both long (15-20 kb) and accurate (>99%) and can be used for comprehensive genomic analysis including de novo genome assembly, structural variant calling and single nucleotide variant calling. Listen to this webinar recording to hear how easy it is to use HiFi reads for de novo genome assembly in humans and across the tree of life, how to evaluate the quality of your HiFi assembly using the three C's: contiguity, completeness and correctness, how the Google AI team retrained DeepVariant, a highly accurate SNP and Indel caller, for PacBio HiFi data and how PacBio HiFi data can improve the Genome in a Bottle benchmark sets

p.pngCheck out this latest preprint describing how Nurk et al. 2020 developed HiCanu for accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Nice to See You, Telomere: Scientists Use SMRT Sequencing for Previously Intractable Regions of the Human Genome. Read about how researchers have used HiFi data to resolve and study telomeres like never before.




Missing Genomes

Where are they? Help us find the high quality reference genomes for Australia and New Zealand indigenous populations! Here is a map of high quality PacBio population-specific genome assemblies from around the world. Contact us if you have found the ones for Australia and New Zealand. Read why we need more diversity in genomic databases in this article by Jonas Korlach, PacBio CSO.

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Epigenetics with SMRT Sequencing

Did you know that you can directly detect epigenetic modifications with SMRT Sequencing? Learn about methylation detection on the Sequel II System and find out how researchers are applying this technique to reveal R-M systems in both viruses and bacteria.

getimage-6.pngLearn how Jensen et al. 2019 used SMRT sequencing for high throughput pairing of methyltransferases and their motifs


getimage-7.pngRead the PacBio Blog about Prokaryotic Methylation Detection on the Sequel II System.


getimage-8.pngExplore this preprint where Jeudy et al. 2019 DNA methylation by MTases encoded in giant virus genomes.




Covid-19 Sequencing Tools and Resources

getimage-9.png Sequencing SARS-CoV-2 - With long-read amplicon sequencing you can gain access to the viral RNA genome.


getimage-10.png Understanding the Immune Response to COVID-19 - With long reads you can sequence full-length B Cell Repertoire and the IGH locus.




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