Conference Announcement | January 12-17, GrandOmics sincerely invites you to participate in the 2024 PAG event!

International Plant & Animal Genome (PAG Conference) is an internationally renowned top academic conference on animal and plant genomics research, held from January 12th to 17th, 2024 in San Diego, CA, USA. The PAG consists of scientific workshops, plenary speakers, industry workshops, digital tools and resources sessions, posters sessions, and exhibits with vendors presenting industry related productions and services. It is designed to provide a forum on recent developments and future plans for plant and animal genome projects. Conference is an excellent opportunity to exchange ideas and applications on this internationally important project. This conference covers the latest research progress in genomics of major crops, cutting-edge developments in bioinformatics and high-throughput sequencing technology, and provides a high-level communication platform for genetic researchers in multiple disciplines and fields.

Meeting Information
Location: San Diego, CA, USA
Time: January 12-17, 2024
Website: https://intlpag.org/31/

Program Overview
Day One / Friday, January 12, 2024

8:00 AM – 9:00 PMMeeting Management Office Open
8:00 AM – 9:00 PMSpeaker Ready Room Open
9:00 AM – 9:00 PMRegistration Open
9:30 AM – 10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
1:30 PM – 3:40 PMWorkshop Session*
2:00 PM – 9:00 PMPoster Hanging Access
3:00 PM – 4:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
Day Two / Saturday, January 13, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:30 AM – 7:00 PMRegistration Open
7:30 AM – 9:00 PMPoster Hanging Access
8:00 AM – 10:10 AMWorkshop Session*
8:00 AM – 12:40 PMWorkshop Session*
8:00 AM – 6:10 PMWorkshop Session*
9:30 AM – 10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
12:00 PM – 9:00 PMPoster Viewing Access
12:00 PM – 1:30 PMLunch
1:30 PM – 3:40 PMWorkshop Session*
1:30 PM – 3:40 PMDigital Tools and Resources Workshop #1
3:00 PM – 4:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:00 PM – 6:30 PMCoffee Break
6:20 PM – 8:30 PMWorkshop Session*
Day Three / Sunday, January 14, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:30 AM – 12:00 PMPoster Hanging Access
7:30 AM – 5:00 PMRegistration Open
8:00 AM – 10:10 AMWorkshop Session*
8:00 AM – 12:40 PMWorkshop Session*
9:30 AM – 10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
12:00 PM – 1:30 PMLunch
12:00 PM – 8:45 PMExhibits Open
1:30 PM – 3:40 PMWorkshop Session*
1:30 PM – 6:20 PMWorkshop Session*
3:00 PM – 4:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:30 PM – 7:15 PMPlenary Lecture – Appolinaire DjikengDirector General, International Livestock Research Institute (ILRI), Kenya
Talk Title: “Livestock and the Food Systems: A Focus on Smallholder Systems in the Global South”
7:15 PM – 8:45 PMOpening Reception
Day Four / Monday, January 15, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:00 AM – 9:30 PMPoster Viewing Access
7:30 AM – 5:00 PMRegistration Open
8:00 AM – 8:45 AMPlenary Lecture – Scott EdwardsProfessor and Chair, Department of Organismic and Evolutionary Biology, Harvard University; Curator of Ornithology, Museum of Comparative Zoology, USATalk Title: “Comparative Population Pangenomes: A New Frontier for the Evolutionary Analysis of Birds”
8:45 AM – 9:30 AMPlenary Lecture – Lucy Van DorpUCL Excellence Fellow, University College London, UKTalk Title: “Tracking Pathogens in Space and Time”
9:30 AM – 11:30 AMCoffee Break
9:30 AM – 5:00 PMExhibits Open
10:00 AM – 11:30 AMPoster Session – Even Numbers
11:30 PM – 1:00 PMLunch
12:50 PM – 3:00 PMWorkshop Session*
12:50 PM – 3:00 PMDigital Tools and Resources Workshop #2
3:00 PM – 4:30 PMPoster Session – Odd Numbers
3:00 PM – 4:30 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:00 PM – 6:30 PMCoffee Break
6:20 PM – 8:30 PMWorkshop Session*
Day Five / Tuesday, January 16, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:00 AM – 3:00 PMPoster Viewing Access
7:30 AM – 3:00 PMRegistration Open
8:00 AM – 8:45 AMPlenary Lecture – Katrien DevosDistinguished Research Professor, University of Georgia, USATalk Title: “Ensuring Food Security in a Changing Climate: Adopt an Orphan” (Preliminary Title)
8:45 AM – 9:30 AMPlenary Lecture – Amy Marshall ColonAssociate Professor, Department of Plant Biology, University of Illinois Urbana-Champaign, USATalk Title: “Integrative Modeling for the Development of in Silico Crops”
9:30 AM – 10:30 AMCoffee Break
9:30 AM – 3:00 PMExhibits Open
10:30 AM – 12:40 PMWorkshop Session*
10:30 AM – 6:10 PMWorkshop Session*
10:30 AM – 12:40 PMDigital Tools and Resources Workshop #3
12:00 PM – 1:30 PMLunch
1:30 PM – 3:40 PMWorkshop Session*
2:00 PM – 3:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:00 PM – 6:30 PMCoffee Break
6:20 PM – 8:30 PMWorkshop Session*
6:20 PM – 9:30 PMWorkshop Session*
Day Six / Wednesday, January 17, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 2:00 PMSpeaker Ready Room Open
7:00 AM – 5:00 PMMeeting Management Office Open
7:00 AM – 12:00 PMPoster Viewing Access
7:30 AM – 12:00 PMRegistration Open
8:00 AM – 8:45 AMPlenary Lecture – Dirk InzeDirector, VIB-UGent Center for Plant Systems Biology, BelgiumTalk Title: “Multiplex Engineering of Yield Traits in Maize”
8:45 AM-9:30 AMPlenary Lecture – Virginia WalbotProfessor Emerita, Stanford University, USATalk Title: “Building a Maize Anther”
9:30 AM-10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
10:30 AM – 12:40 PMDigital Tools and Resources Workshop #4
12:00 PM – 1:30 PMLunch
7:15 PM – 11:55 PMBanquet Dinner

Join us in #PAG31
Our booth No. 504
Excited to see you here!

We will participate with you to explore the application of multi-omics technologies in animal and plant research, and work together to promote the development and innovation of genomics, with our extensive reading of omics products and experience in animal and plant genome projects!

GrandOmics X PacBio Revio – Higher throughput, more HiFi reads, but cost effeciently

GrandOmics is happy to share that two latest PacBio sequencers -Revio have arrived on 4 Arpil. The new platforms provide 15-fold increase in productivity compared to Sequel II/IIe, shortening turnaround time and reducing cost by almost 3-fold.

The Revio system uses a high-density, 25 million SMRT Cell, up to 4 SMRT Cells in parallel sequencing to provide 360 Gb of HiFi reads per day. In addition, With the Revio system, you can achieve higher throughput to support large studies and develop novel applications.

GrandOmics is releasing sequencing services using this latest sequencing platforms by Revio:

  • Genome Sequencing
  • Single Cell Full-length Transcriptome Sequencing
  • T2T assembly
  • Pangenomic Sequencing
  • Metagenomics Research

… More to explore.

Contact us: inquiry@grandomics.com

GrandOmics collaborates with Oxford Nanopore to deliver dbSV-100k, a project to deliver 100,000 affordable nanopore long-read human genomes

Strategic collaboration between two organisations represents largest nanopore sequencing project to date, capitalising on recent developments bringing ultra-high yields with PromethION

GrandOmics, a leading sequencing company in China, has announced a populational-scale project, dbSV100k, to understand the impact of structural variation on human disease. The project aims to sequence 20,000 human genomes in 2019, with a goal of 50,000 by the end of 2020 and total of 100,000 by the end of 2021. This uses high-throughput nanopore sequencing on the PromethION device and the project will explore viable opportunities for the development of clinical applications, with a view to ultimately providing clinical genetic diagnosis services in the future.

This research project aims to gain a complete understanding of genetic variations associated with human health and disease. Oxford Nanopore has entered into a Memorandum of Understanding with GrandOmics in support of their plan to build genome medicine services at an affordable price with high-quality that is accessible for anyone, anywhere.

The highest yields, with long reads

The performance of PromethION, the newest nanopore sequencing device, has now accelerated sufficiently to allow >7Tb on human samples using a complete set of 48 flow cells – the equivalent of 86Gb of real time sequencing data per hour, or ~1 human genome at 30X coverage.

PromethION, as with other nanopore sequencers, sequences the complete nucleic acid fragment and therefore provides very long reads – the current record is 2.3Mb in a single read and this represents the full fragment rather than multiple repeat passes of a smaller fragment.  With real time data and modular flow cells, the performance of the technology has developed while flow cell costs have remained the same. Flow cells now deliver ultra-high yields, and the latest R10 nanopore has delivered Q50 (99.999% consensus accuracy) in a small genome in internal company experiments. R10 is now being trialled by GrandOmics.

GrandOmics: delivering high throughput nanopore genomics

To date, GrandOmics has sequenced more than a thousand human genome samples (G1k) and several hundreds of plants, animals, and microbial genomes using nanopore technology, servicing a network of over a thousand customers throughout the world. This has resulted in new discoveries in genome science and genomic medicine, in more than 50 publications for the last two years. This includes publications using nanopore technology, with more prospect papers in the near future.

This high-throughput infrastructure will be expanded to deliver dbSV-100K.

“GrandOmics’s mission is to provide innovative and precise genomics solutions for disease research and diagnosis. We have been running our PromethION devices to full capacity, and have developed our own bioinformatics pipelines to drive breakthrough projects to achieve new standards.” Said Mr. Depeng Wang, CEO of GrandOmics.

Dr. Gordon Sanghera, CEO of Oxford Nanopore said: “We are glad to form a strategic and ongoing collaboration with GrandOmics to support genomic medicine and personalized medicine for China. At Oxford Nanopore last week, the PromethION 48 has achieved 7.3Tb of data using a single set of 48 flow cells, and our development pathway offers higher future capacity. We are excited to see GrandOmics drive innovative solutions for offering accessible ‘de novo personal genomes’ to customers using high-throughput PromethION sequencing.”

“This is so far the largest high-throughput nanopore sequencing project in the world, and is the outcome of extensive effort between two parties in developing a strategic alliance for the last several months. This is achieved by a shared vision to create an opportunity to revolutionize genome medicine in the UK, China and the rest of the world.” Min S. Park, Director of GrandOmics Institute.

About GrandOmics

GrandOmics is a world-leading sequencing company in Beijing, China. It was one of the earliest to apply nanopore technology for commercial DNA sequencing in the world, and also the first in China and the second in the world to be certified to provide PromethION sequencing services using Nanopore technology.

GrandOmics provides comprehensive solutions for genome science and genomic medicine. The company aims to utilise advanced sequencing-based solutions for rare genetic diseases, complex diseases, microbial diseases, and cancer, by integrating nanopore long reads and optical mapping to detect and characterize complex mutations in clinical samples of patient genomes. GrandOmics has been establishing one of the world’s largest nanopore long-reads based structural variation databases (www.dbsv.com).

NextOmics, a subsidiary company of GrandOmics, has one of the most complete third-generation sequencing, optical and 3D mapping platforms. NextOmics delivers genome assemblies and analysis pipelines for animal, plant, microbial and human genomes, in research areas such as transcriptomics, metagenomics and epigenetics.

About Oxford Nanopore 

Oxford Nanopore Technologies aims to disrupt the paradigm of biological analysis by making high performance, novel DNA/RNA sequencing technology that is accessible and easy to use. Our goal is to enable the genetic analysis of any living thing, by any person, in any environment.

Our novel, electronics-based DNA/RNA sequencing technology is being used in more than 80 countries, for a range of biological research applications and is also being explored beyond research.

Oxford Nanopore’s proprietary technology is fully scalable for any requirement. Small formats such as Flongle address the need for on-demand, rapid, smaller tests or experiments, and can be used in labs or in the field. The pocket-sized MinION is a powerful and portable sequencing device that can deliver high volumes of long read sequence data. The benchtop GridION X5 can run up to five MinION Flow Cells at a time, on-demand, for larger genomics projects. The recently launched PromethION is the largest format for nanopore sequencing, designed to offer on-demand use of up to 24 or 48 flow cells – each of which can offer more than 100Gb of sequencing data in field.

Global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana using PacBio sequencing Nextomics program

In April 2018, Nextomics joins hands with research group of Xiaofeng Gu, biotechnology research institute, Chinese academy of agricultural sciences, and research group of Hao Yu, department of biological sciences and Temasek life sciences laboratory, National University of Singapore, to publish a paper titled as “DNA N6-Adenine Methylation in Arabidopsis thaliana in the journal of Development Cell. This research reported that global profiling of 6mA sites at single-nucleotide resolution in the genome of A. thaliana at different developmental stages and ecotypes using single-molecule real-time sequencing.

This is the first research article of distributing eukaryote methylation mapped by PacBio SMRT.

Highlights

  • DNA methylation on N6-adenine (6mA) widely occurs in the Arabidopsisgenome;
  • 6mA is more enriched on gene bodies than intergenic regions;
  • 6mA is a dynamic DNA modification during Arabidopsisdevelopment;
  • 6mA is associated with actively expressed genes in

Results

6mA widely occurs in the Arabidopsis genome

Dot blot analysis of gDNA extracted from 3- to 21-day-old Col wild-type plants revealed a gradual increase in the 6mA signal intensity from vegetative to reproductive stage (Fig.1).

Fig. 1 6mA Occurs in Arabidopsis Genomic DNA

Genome-Wide Mapping of 6mA in Arabidopsis sequenced by PacBio SMRT

Compare the dynamic and distribution of 6mA in D9 and D21, and combined with the transcriptome data researchers revealed the function of 6mA during the development of Arabidopsis (Fig.2).

Fig.2 Circos plots of 6mA DNA methylation profiles of 9- and 21-day-old Col wild-type Arabidopsis.

6mA is more enriched on gene bodies than intergenic regions

6mA distribution in Col genomic regions divided into gene bodies, promoters, 5’intergenic, 3’intergenic, and other intergenic regions. The results showed that 32% of 6mA sites were located within gene bodies, and protein-coding genes contained more than half of the 6mA sites in all methylated genes (Fig. 3).

Fig. 3 Distribution Pattern of 6mA Methylation in Genomic DNA of 9-Day-Old Col Plants

6mA is a dynamic DNA modification during Arabidopsis development

Genome-wide mapping of 6mA in gDNA from 21-day-old Col wild-type plants at the reproductive stage by SMRT sequencing identified 184,633 6mA sites, among which 9,909 sites were overlapped with those in 9-day-old plants (Fig. 4), which implied that 6mA DNA methylation positively correlates with the transition from vegetative to reproductive growth.

Fig.4 Venn diagram comparison of the numbers of 6mA sites in D9 and D21.

6mA associated with actively expressed genes in Arabidopsis

Analysis of 6mA methylomes and RNA sequencing data demonstrates that 6mA frequency positively correlates with the gene expression level and the transition from vegetative to reproductive growth in Arabidopsis (Fig. 5).

Fig. 5 Correlation between 6mA and Gene Expression in Col Plants.

This research uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, suggesting that 6mA serves as a hitherto unknown epigenetic mark in land plants. Nextomics took part in the program and provided technical support.

Reference

Liang et al., DNA N6-Adenine Methylation in Arabidopsis thaliana, Developmental Cell (2018), https://doi.org/10.1016/j.devcel.2018.03.012

Other eukaryote methylation published papers

[1]Greer, E.L. et al. DNA methylation on N6-adenine in C. elegans. Cell 161, 868–878 (2015).

[2]Wu, T.P. et al. DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature 532, 329–333 (2016).

[3]Mondo, S.J. et al. Widespread adenine N6-methylation of active genes in fungi. Nature Genetics (2017).

2.2Mb! Nanopore sequencing set a new record for the length of single continuous sequence!

The first >2Mb continuous DNA read sequence has been reported by Oxford Nanopore sequencing technology, which is regarded as another giant leap in the development of Nanopore sequencing. The result was published on BioRxiv by a team at the University of Nottingham, led by Alex Payne, etc.[1]

The output data of NanoporeMinION sequencing is in fast5 format, which can be further converted into fastq format through the base-calling procedure. Previously, the MinKNOW was the conventional choice for MinION base-calling. But Alexander Payne found that the MinKNOW may interrupt long reads by error, while they eliminated this “bug”, the length of reads can achieve over 2Mb.

Why long reads?

Traditional short-read DNA sequencing technologies (also known as the Next-Generation Sequencing, NGS) may provide data about the small fragments of genomic DNA sequences, and it is a great challenge for researchers to assemble these large number of small pieces into a complete genome or dataset.

Nanopore sequencing technology has significant advantages in sequencing read length, including greatly improve the continuity of genome assembly and overcome the problem that caused by complex repeat sequences or structural variation which beyond the capabilities of short-read sequencing. The article recently published on Nature Biotechnology about human Y chromosome centromere sequences achieved by Nanopore sequencing have emphasized the abilities of Nanopore sequencing in solving complex repetitive regions. In addition, the identification of complex tandem rearrangement in the nematode genome and structural variations in the drosophila genome are all outstanding applications of Nanopore long reading sequencing. (For more details, see the “extended reading” at the end of this article)

As the first third-generation sequencing company with the Nanopore sequencing platform in China, NextOmics Biosciences have obtained a great amount of excellent data. Here we present you some results.

Case one: Assembly of an insect’s genome by Nanopore sequencing

The size of the insect genome was estimated to be ~ 330Mb based on k-mer analysis

Fig. 1 K-mer analysis

Qualified sample DNA was extracted, and 30Gb of third-generation data were sequenced on the Oxford Nanopore GridlON X5 platform, with a maximum reading length of 270Kb, and reads N50 length was 26.8kb. Long read length is a prerequisite for more accurate genome assembly.

Fig. 2 Distribution of read length

Genome assembly applying a variety of software and select the optimal scheme. The ultra-long read Nanopore sequencing matching super-computing platform enables genome assembly to be more continuous and faster. In this case, Contig N50 can be >7mb, which has reached the high-quality assembly level as insect model animal fruit flies.

Table1 The assembly results

The assembled genome was compared with the insect genome database by BUSCO to assess the integrity of the assembly of conservative genes, and the entire genome was reflected by indirect measurement f. The results show that after Nanopolish+Pilon (* 2) correction, BUSCO evaluation can reach ~ 98% and genome assembly integrity is good.

Table2 BUSCO assessment

Case 2: Ultra-long sequencing data from an animal

Nanopore ultra-long sequencing can achieve ultra-long reading length. Based on its unique transposase library, DNA sequencing library containing ultra-long fragments, and the ultra-long DNA sequence can be obtained by Nanopore sequencing. Ultra-long sequences will greatly facilitate the de novo assembly of genome and the identification of complex structural variations (SVs) of chromosomes.

Fig. 3 Process of Ultra-long library construction

NextOmics Bioscience conducted ultra-long library construction and sequencing on the blood of a mammal based on Nanopore sequencing platform. The reads N50 of multiple libraries were longer than 70kb, and the longest read length was more than 1Mb.

Fig. 4 Library reads N50 (partial)   

   Fig. 5 Distribution of read-length in a library

[1]Payne, A., Holmes, N., Rakyan, V. & Loose, M. Whale watching with BulkVis: A graphical viewer for Oxford Nanopore bulk fast5 files., doi:10.1101/312256 (2018).

Long-read sequencing technology generate a heated discussion in The Jackson Laboratory

As a large number of highly impact articles which based on the long-read sequencing technology were published, the world’s top medical genomics Laboratory The Jackson Laboratory for Genomic Medicine held a long-read sequencing workshop on April 23 to 25, 2018. Hundreds of experts and scholars in the field of biology, bioinformatics, medical genetics from across the globe had gathered in Farmington CT to discuss about the technology and molecular biology driving each sequencing platform, including those from Pacific Biosciences, 10X Genomics, and Oxford Nanopore. Prof. Kai Wang, chief scientist of NextOmics Bioscience (China, Wuhan), gave an excellent presentation about the detection of structural variations (SVs) in human genome via different long-read sequencing platforms and win a high praise.

This academic symposium mainly focused on the latest technologies such as PacBio, Oxford Nanopore, 10X Genomics, Bionano and Hi-C etc. The chief scientist of NextOmics Bioscience (China, Wuhan), Professor Kai Wang, was invited to give a talk on the topic “Long-Read Sequencing Meets the Human Genomics”. He clarified the characteristics and advantages of applying Nanopore, PacBio and Bionano technologies to detect human genome SVs. Then he introduced a new algorithm which broke through the present technical bottlenecks of microsatellite sequences repeat unit identification based on PacBio Sequencing, RepeatHMM, developed by his team. In addition, he also declared a detection technology of facial shoulder brachial muscular dystrophy (FSHD) based on Bionano SaphyrTM platform perfectly solves the existing problems of FSHD diagnosis. It is worth mentioning that Prof. Wang’s idea of focusing on long-read sequencing techniques to study SVs coincides with Michael Schatz, a renowned scientist in computer science and biology at Johns Hopkins university. And Dr. Yijun Ruan, the director of genomic science department belongs to The Jackson Laboratory, talk about the Hi-C technology, he focused on the applications of Hi-C in analysis of genomic SVs, interactions in transcriptome, and the modification of genome etc. He provided a new insight about genome research by the perspective of three-dimensional level. Beyond that, many experts and scholars had introduced new bioinformatics algorithms to participants, such as associate professor Winston Timp, the department of biomedical engineering at Johns Hopkins university, showed their latest tools based on Nanopore for characterizing the genome and epigenome.

The Jackson Laboratory

The Jackson Laboratory is an independent, nonprofit biomedical research institution dedicated to the discovery of precise genomic solutions for human disease.

For more details: https://www.jax.org/

Nextomics Biosciences

Nextomics Biosciences, founded in 2011 in Biolake, Wuhan, is a worldwide third generation sequencing (TGS) leader, which has branches in Beijing Life Science Park and Philadelphia, the US. It owns the largest TGS center in China & the US, and 8Tb TGS data could be yielded monthly and more than 20 TGS sequencers are now in operation.

As the first provider of third-generation sequencing service in China, Nextomics has successfully developed bioinformatics analysis pipelines based on PacBio SMRT sequencing technology since 2013 and launched Sequel genomic center since 2016. Significantly, Nextomics has become the first in China and one of the first in the world certified Nanopore service providers since 2017. Nanopore sequencing can provide extremely long read lengths to make genome assembly more accurate and simpler through MinION, GridION, and PromethION, and especially, it can offer the real-time direct RNA sequence. Nextomics has depth of TGS experience and has completed over 4,00 hundreds of genome projects ranging from de novo genome assembly to full-length transcriptome analysis and metagenomics, which is always focusing on meeting the demands of customers and updating the technologies of TGS.

NextOmics has established a comprehensive and cutting-edge omics research center by using a variety of technologies, such as the Oxford Nanopore, optical mapping (BioNano), PacBio sequencing and High-throughput chromosome conformation capture (Hi-C). In 2018, NextOmics will also leverage Nanopore Technology in areas such as Ultra Long Reads, direct RNA sequencing and DNA/RNA modifications. We sincerely welcome worldwide customers and collaborators to work with NextOmics and enjoy the unique advantages of long read sequencing. Let’s embrace the long-read sequencing era!

PacBio also Updated at last! Both Software and Reagent, for Higher Throughput and Longer Reads!

Pacific Biosciences of California, Inc. formally announced a new version of Sequel® Software (V5.1) and a new polymerase on Mar. 7, 2018. Combined, these enhancements increase throughput and the overall performance of Single Molecule, Real-Time (SMRT®) Sequencing for key applications such as de novo assembly, structural variant detection, targeted sequencing, and RNA sequencing (Iso-Seq® method), making genomic research more economical.

With this release the Sequel System can achieve up to 10 Gb per SMRT Cell for genomic libraries, effectively doubling the throughput when using ultra-long inserts (>40 kb) for de novo genome assembly. For targeted and RNA sequencing, customers can achieve up to 20 Gb per SMRT Cell.

For human whole genome sequencing (WGS) studies, the new improvements support sensitive detection of structural variants with as little as 5- to 10-fold coverage per individual. As a result, customers can now complete low-cost WGS studies in thousands of individuals using fewer SMRT Cells.

For long amplicons (>3 kb), the new polymerase increases the number of high-quality sequences per SMRT Cell, reducing costs for HLA sequencing and other targeted applications. Further, software enhancements for multiplexed samples simplify the analytical workflow.

Appendix: Based on PacBio SMRT technology, NectOmics has assembled hundreds of genomes and authored mature process for full-length transcriptome, some published papers as follow:

Classic NextOmics genome-assembling projects

Classic NextOmics Full-length Transcriptome projects based on the Third Generation Sequencing Technology

NextOmics: the FIRST officially certified service provider of Oxford Nanopore sequencing in China


NextOmics, a subsidiary of Beijing GrandOmics Biosciences, has become the first officially certified service provider of Oxford Nanopore sequencing in China. NextOmics has established the Oxford Nanopore sequencing platform since September 2017, and has finished a few dozen pilot projects so far with outstanding yield and data quality. Currently, NextOmics has eleven GridIONs and two MinIONs in operation, with more sequencers on order. Additionally, a PromethION is expected to be deployed soon by NextOmics to provide high quality and high throughput sequencing services for worldwide researchers.

NextOmics started to offer Nanopore sequencing service to Chinese and worldwide customers in 2017, and has processed different types of samples such as mammals, plants and insects. As of January 17, 2018, The NextOmics Nanopore Sequencing Center has yielded more than 2Tb qualified data within a 4-month period. In particular, NextOmics has completed the sequencing and genome assembly of over 20 plant and animal species, with significantly improved assembly quality compared to previous generation of sequencers.

NextOmics has focused on offering  professional and extraordinary genome sequencing solutions of Third Generation Sequencing (TGS)/Nanopore Sequencing, especially on areas of complex genome sequencing and assembly. At the International Conference of Plant and Animal Genomics 2018 (PAG XXVI), NextOmics released the genome skimming result of Paris japonica, the largest genome (~152Gb) in the planet earth. In the past 8 years, NextOmics has participated in over 300 genome sequencing projects and published many influential research articles, such as the first de novo near-complete genome of a Chinese individual, the first near-complete Indica rice genome, the first firefly genome, and the first Eucommia ulmoides genome. In the National Plant Biology Conference 2014 (Hefei, China), NextOmics firstly proposed the “1Mb Contig N50” slogan. Now, with the arrival of Oxford Nanopore Technology, megabase-sized  contig N50 in most species will be very common in the future.

NextOmics has established a comprehensive and cutting edge omics research center by using a variety of technologies, such as the Oxford Nanopore, optical mapping (BioNano), PacBio sequencing and 3D genome mapping. In 2018, NextOmics will leverage Nanopore Technology in areas such as direct RNA sequencing and DNA/RNA modifications. We sincerely welcome worldwide customers and collaborators to work with NextOmics and enjoy the unique advantages of long read sequencing. Let’s embrace the Nanopore era!