I might have New Zealand’s first #pacbio #revio?

Onso remains to be built

I'm excited to be back in person this year with some really interesting things to talk about. With researchers at Boston Children's Hospital and Harvard Medical School, we generated HiFi WGS datasets for a set of 10 probands with sensorineural hearing loss unexplained by srWES and srWGS.

We found candidate variants consistent with the phenotypes in several samples, and I'll be sharing three examples in poster P16.011.D on Monday and workshop W09 on Sunday.

#ESHG2023 #PacBio

Heading up to Glasgow for ESHG2023. If you'd like to talk about rare disease analysis using PacBio HiFi reads, or even just long read variant calling more generally, please reach out and we'll find some time to meet.

#ESHG2023 #PacBio

#Minimap2 #Rust library release: minimap2 v0.1.13+minimap2.2.26

* Latest minimap2 stable release (2.26)
* with_seq function
* hopefully compiles for MacOS / aarch64.
* Still struggling with SSE, I recommend using simde feature
*Soft-clipping properly in CIGAR strings but use caution. Happy to work on it more.

https://github.com/jguhlin/minimap2-rs

https://crates.io/crates/minimap2

And the -sys crate
https://crates.io/crates/minimap2-sys

#bioinformatics #genomics #nanopore #pacbio

The NZ #PacBio Sequencing Experience Tour, featuring a #Manel who were planning to speak in the Federation of Women room, has been postponed due to scheduling issues with the speakers.

We hope that the comparative genomics analyses made available through this study will provide a route towards the application of genomics-informed conservation programmes across the great diversity of invertebrate species. A big thank to all the amazing people from the Darwin Tree of Life Project that made this reserch possible! #biodiversity #conservation #comparativegenomics #PacBio #DarwinTreeofLife #Ensembl #emblebi #sangerinstitute #wellcometrust

RT @hagentilgner
Andrey & Alla put out the newest version of Isoquant
(https://www.nature.com/articles/s41587-022-01565-y); Results unchanged but memory usage down ~10-15 fold and disk usage down ~5-fold;
https://github.com/ablab/IsoQuant/releases/tag/v3.2.0
#LongRead #RNA @iRnaCosi
#nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing

Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries.
Our pre-print is now available: https://www.biorxiv.org/content/10.1101/2023.02.22.529427v1

@fritzroth
#pacbio #Bioinformatics #DeepMutationalScanning #BarSeq #VariantEffectMapping #longread #mave

Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries.
Our pre-print is now available: biorxiv.org/content/10.1101/2023.02.22.529427v1

@fritzroth
#pacbio #Bioinformatics #DeepMutationalScanning #BarSeq #VariantEffectMapping #longread #mave

Hey everyone!

I'm a #bioinformatician who works in the mycology and microbiology lab.

Until recently, I have primarily worked with #rnaseq #eDNA #metabarcoding analysis. I'm also learning how to create new tools and establish a pipeline centered on #Pacbio long read sequencing equipment.

I primarily program in #python, #bash, and #R.

I appreciate #technology and #AI as well, and I'm curious how far it will impact our daily life.

Let's #PAG30 with FAANG Session!
I'll present my work on chicken and pig genomes and #PACBIO ISOseq tomorrow. See you there!

RT @hagentilgner
Out in @NatureBiotech: What isoforms are really in your @PacBio or @nanopore run? Andrey&Alla (with help by @noush_joglekar, AS, @jjarroux &AL) have precise answers:
https://www.nature.com/articles/s41587-022-01565-y
#LongRead #RNA @iRnaCosi #nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing

RT @hagentilgner@twitter.com

Out in @NatureBiotech@twitter.com: What isoforms are really in your @PacBio@twitter.com or @nanopore@twitter.com run? Andrey&Alla (with help by @noush_joglekar@twitter.com, AS, @jjarroux@twitter.com &AL) have precise answers:
https://www.nature.com/articles/s41587-022-01565-y
#LongRead #RNA @iRnaCosi@twitter.com #nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing

🐦🔗: https://twitter.com/hagentilgner/status/1610275737562673153

RT @hagentilgner
Out in @NatureBiotech: What isoforms are really in your @PacBio or @nanopore run? Andrey&Alla (with help by @noush_joglekar, AS, @jjarroux &AL) have precise answers:
https://www.nature.com/articles/s41587-022-01565-y
#LongRead #RNA @iRnaCosi #nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing

Out in @NatureBiotech: What isoforms are really in your @PacBio or @nanopore run? Andrey&Alla (with help by @noush_joglekar, AS, @jjarroux &AL) have precise answers:
https://www.nature.com/articles/s41587-022-01565-y
#LongRead #RNA @iRnaCosi #nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing

We successfully used it on #MiSeq, #PacBio, and #Nanopore datasets from blood samples from people with Huntington’s disease or Fuchs endothelial corneal dystrophy.

It stacks up to other current algorithms but it shines in that it can be used used on data from any of these and from any locus you are interested in.

It also identifies interruptions, both known and unknown and lets you evaluate the extent of repeat size mosaicism.

The code lives here:
https://github.com/DionLab/RepeatDetector

RT @AhmadAlKhleifat@twitter.com

Delighted to host Dr Michael Eberle @MikeEberle@twitter.com Vice President of Computational Biology at @PacBio@twitter.com on 6 December (2-3pm GMT) in @kingsmnd@twitter.com @KingsIoPPN@twitter.com to discuss: “Resolving the informatics gaps to build the fully featured genome”. DM me if you want to attend the seminar. #PacBio

🐦🔗: https://twitter.com/AhmadAlKhleifat/status/1598616876187353089

#Introduction

Hi! I am a chief scientist at the National Cancer Center Research Institute in Japan.
My research area is #bioinformatics and #statistics with a focus on #cancergenomics.

Recently, I’ve been interested in the systematic identification of #splicing variants (recent paper: https://www.nature.com/articles/s41467-022-32887-9).
I am also developing software for long-read sequencing analysis (e.g., #nanopore and #PacBio) (recent preprint: https://github.com/friend1ws/nanomonsv).

I'll be presenting work on the tool Paraphase for #SMN calling tonight at #biodata22 poster 91. I'm virtually attending due to illness, so if you wish to learn more about how we're leveraging #PacBio #HiFi data to resolve complex, clinically significant variation in SMN1/2, come "find" me on #biodata22's slack, Twitter, or Mastodon!

Tychele Turner #biodata22 with "Precision genomics as a key component for the future of precision medicine".

Interested in precision genomics, today focusing on using #PacBio #HiFi to solve unsolved autism case. Workflow involving both assembly- and reference-based processes.

Long reads allowed them to identify and phase a mosaic, de novo variants onto parental strand. Also able to resolve complex translocations in 9p minus syndrome (complex rearrangements shown on screen).