PacBio - Monthly Newsletter (August)

pacbio_shortlogo_color_rgb-01.jpgWelcome to the PacBio News and Events Update!


Are You Using HiFi?

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Events and Webinars

Webinar TODAY! For Bioinformatics - User-friendly Solutions to SMRT Sequencing Bioinformatics with SMRT Link

Date: Thursday 13th August, 2020
Time: 12:00pm AEST

khi-pin-chua.jpeg Speaker:

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


In this webinar we will cover:

  • Introduce SMRT Link as the comprehensive workflow manager for all SMRT Sequencing applications.
  • Cover the main analysis pipelines for different applications.
  • Review the changes in the latest version v9.0.
  • Cover new recommendations for selected analysis pipelines.
  • Discuss command line alternatives to selected SMRT Link pipelines

Register Now



Past Webinar Recordings:

Listen to our CSO Jonas Korlach discuss the applications of HiFI reads.

View Recording


PacBio APAC Webinar by Dr. Adam Ameur of SciLifeLab shared his work at SciLifeLab including how SMRT Sequencing has been applied in many different projects; from the sequencing of single genes, to de novo assembly of complete human genomes and a new method to study CRISPR-Cas9 off-target effects using long reads

View Recording




Recent Blogs

Sequencing 101: What's the Value of Sequencing Full-Length RNA Transcripts?

While different tissues in an organism may share the same genomic DNA, they can differ greatly in what regions are transcribed into RNA and in their patterns of RNA processing. By reviewing the history of transcriptomics, we can see the advantages of RNA sequencing – using a full-length transcript approach – become clearer.

Read the Full Post



Review: How Long-Read Sequencing Is Revealing Unseen Genomic Variation

variants-diagram.pngIn a review, University of Washington scientists give credit for accomplishments in filling the gaps in genomic variant identification to advancements in long-read sequencing.


Read the Full Post



New Isoform Phasing Technique Traces Parental-Progeny Differences In Maizes

corn.jpegCold Spring Harbor scientists have performed an isoform-level phasing study in maize using the PacBio Iso-Seq method and a new tool, IsoPhase.


Read the Full Post



A HiFi View: Sequencing the Gut Microbiome with Highly Accurate Long Reads

Whether you are seeking to characterize microbial diversity in the gut, or distinguish between pathogenic and commensal bacteria on the skin, full-length 16S rRNA sequencing using PacBio systems is a valuable tool for metagenomics studies, according to microbiology researchers in a recent webinar.

Read the Full Post




Bioinformatics Resources

HiFi Datasets: Highly accurate long reads, or HiFi reads, have the ability to resolve some of the most challenging regions of the human genome and detect previously inaccessible variants. They offer read lengths of up to tens of kilobases with accuracy on par with short reads. Explore some publicaly available HiFi datasets across numerous applications, including human WGS. Explore HiFi Datasets

Workshop materials: UC Davis Bioinformatics Core has recently organized a workshop on genome assembly. Sarah Kingan and Ivan Sovic from PacBio were invited to teach how to assemble HiFi genomes using IPA. Materials with useful information are freely available on UC Davis's website.

De novo assembly tool: A new release of Hifiasm 0.9 is now on github. This release reduces mis-assemblies and improves on assembly completeness!




Recent Publications

Human Biomedical

Recommended Review: Long-read human genome sequencing and its applications. Nature Reviews Genetics.
Read More.

Genome in a Bottle (GIAB): A new preprint on the latest update to Genome in a Bottle (GIAB) datasets used for variants benchmarking. This dataset is important to assess the accuracy of variant calling in human sequencing. PacBio HiFi reads were instrumental in allowing the consortium to expand the benchmark.
Read More

The Telomere to Telomere (T2T) consortium revealed their full assembly of the human X chromosome (chrX) in Nature.  They chose the chrX for the manual finishing and validation.  It was broken in just 3 places and while ultralong ONT was important to getting it stitched together, HiFI reads are what enabled them to correctly call the sequence of two nearly identical 100kb+ segmental duplications that broke the assembly and to decipher the exact sequence of the repeat arrays found in the centromere. 
Read More

There is a Nature Medicine paper published on July 10.  The team at Vanderbilt combined Berkeley Light's single cell system with PacBio Sequel to identify a panel of mAb towards SARS-CoV-2 spike protein.  As far as I know this is the first study where PacBio was combined with Berkeley Light's technology.  A very exciting application indeed.
Read More

A bit older but a good one: Improved assembly and variant detection using HiFi reads.
Read It Here



Microbiology

Finishing draft genomes provides access to biosynthetic gene clusters
Read It Here!

B. cenocepacia methylation data adds insights on biofilm formation.
Read It Here!

Gene duplications and expansions revealed with phased long-read assemblies.
Read It Here!



Plant and Animal

The sound of pangenome buzzword is drumming up.

Plant pan-genomes are the new reference
Edwards, Batley
Read It Here!

Pan-genomics in the human genome era
Sherman & Salzberg
Read It Here!

There is also an excellent bat pan-genome paper that appeared in Nature. 
Six reference-quality genomes reveal evolution of bat adaptations
Read It Here!
CLR for assembly and Iso-Seq for genome annotation

Identifying the role of alternative splicing for modulating response to nitrogen in maize Read it here!




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