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PacBio Newsletter _Jan 2021

2021-01-20 08:26:51    Source:Gene Company Limited

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Pacbio Updates


The 1st PacBio APAC Webinar of 2021

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DATE: Thursday, 28 January 2021

TIME: 2 -3 pm (HK time)


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In this webinar, you will explore:

Recommendations and best practices for wet-lab workflows to generate the highest quality HiFi metagenomic data using PacBio Sequel system

Bioinformatics workflow starting from CCS to command line analysis of HiFi data. 

Shotgun metagenomics analysis to demonstrate how the high accuracy of HiFi sequencing allows the assembly of many complete or near-complete metagenomic-assembled-genomes (MAG).



Speaker

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Khi Pin Chua, Ph.D.
Scientist I
Field Applications Support, Bioinformatics
PacBio Asia Pacific


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Minning Chin
Field Applications Support
PacBio Asia Pacific


PAGBio Day 2021 - PacBio Plant and Animal Genomics Day


Tuesday, 20 January 2021, 1-5am (HK time)


The event will also be recorded and available on demand upon registration.


Join this virtual half-day event to hear from fellow scientists on their latest discoveries, learn how you can use HiFi sequencing to advance your research, and engage with the scientific community.   

 

Live keynote session and panel discussion on the future of sequencing in Plant and Animal Genomics

Exciting talks from PacBio users on their latest research 

Application workshops – sharing workflow best practices

Opportunity to connect with colleagues in the PAGBio Day Community

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PacBio Sequel IIe in Well-known Genome Project


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PacBio Sequel IIe in Well-known Genome Project

The world-leading Wellcome Sanger Institute invested seven more new PacBio Sequel IIe Systems to support Darwin Tree of Life – a project to sequence the genomes of all 60,000 species of eukaryotic organisms in Britain and Ireland.


This investment expanded the generation of high-quality genomes with HIFI reads for improving fundamental understanding of biology and aiding biodiversity conservation.


For more details, please click HERE


LAST CALL!

2020 HiFi FOR ALL – Collaborations SMRT Grant Program


Deadline is approaching. Submit your 500-word proposal by January 22, 2021


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Learn more and apply at pacb.com/smrtgrant


Protocol/document Updates


Protocol/document releases from Nov 2020



Protocols

Released date

Changes

Overview   – Sequel Systems Application Options and Sequencing Recommendations

December   3, 2020 

Added   information including IPA for genome assembly, pbaa for amplicon analysis, no amp workflow   is now supporting up to 48 samples/ cell

Operations   Guide – Sequel II and Sequel IIe   Systems: The SMRT Sequencers  

November   16, 2020  

Updated   for Sequel IIe System; Added Pacific Biosciences logo   to front cover.  


Guide   – Sequel II and Sequel IIe   System Safety  


November   16, 2020  


This   guide provides important safety information on the Sequel® II and

Sequel   IIe Systems from Pacific Biosciences. It   also provides product compliance and regulatory statements. Read this   document before performing any procedures on the Sequel II or Sequel IIe   Systems.

Quick   Reference Card – Loading and Pre-Extension Recommendations for the Sequel II   and IIe   Systems  

November   16, 2020  


Version   05; Updated to add Ultra-Low DNA and several other parameter changes.  




Publication Highlights

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Science. 2020 Dec 18;370(6523):eabc6617. https://science.sciencemag.org/content/370/6523/eabc6617.long


The rhesus macaque (Macaca mulatta) is one of the most widely used nonhuman primate (NHP) models for studying human biology and disease.


In this study, with applying PacBio long-read sequencing platform, the genome of the rhesus macaque is refined and so the reference qualities approach the human genome, contributing to improved genome quality, gene annotation and sequence diversity in macaques.


This new genome nearly matches two human genome (GRCh38) builds in contigN50. PacBio generated genomes in blue had very low number of contig gaps. (Fig. 1) Overall contiguity increased by 120- and 5.6-fold compared with the previous Indian (Mmul_8.0.1) and Chinese (rheMacS) rhesus macaque assemblies, respectively.


With the gene annotation using  6.5M IsoSeq read, 550 gene structures were demonstrated to split over multiple contigs, and 827 protein-coding genes show evidence of being part of gene families that exhibit reduced copy number in this assembly relative to that of humans, with 473 of those showing a 2-1 relationship and 295 being 3-1 in humans compared with macaques.


Examples of gene annotation: new gene model which is homologous to the cytochrome gene and two macaque isoforms of tropoelastin gene with two novel exons in Fig 2.


With a better genome, short read WGS genomes of 850 macaques (mostly captive USA research colonies but a couple wild caught) were aligned to study the sequence diversity amongst live animals. It was found that an average research macaque carried 9.7M SNVs, almost twice as diverse as humans.


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Fig.2


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DNA Shearing tools for Whole Genome Sequencing

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Contact us to get a product catalogue to learn more!

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