Pacbio Updates

The 1st PacBio APAC Webinar of 2021

DATE: Thursday, 28 January 2021

TIME: 2 -3 pm (HK time)

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

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

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

PacBio Sequel IIe in Well-known Genome Project

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

Learn more and apply at pacb.com/smrtgrant

Protocol/document Updates

Protocol/document releases from Nov 2020

Publication Highlights

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.

Fig.2

DNA Shearing tools for Whole Genome Sequencing

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