Discover and read the best of Twitter Threads about #nanopore
Most recents (13)
Happy to announce that the full genome sequence of the Cambodian #H5N1 #avianflu case is now available on @GISAID. This has been an incredible effort by a number of people: (1/)
We were able to go from original sample to full genome sequence in <24 hours using iMS-PCR from @peter_thielen from @JHUAPL on @oxfordnanopore #ONT technology @nanopore #nanopore using capacity developed before and during the #COVID19 pandemic (2/) 
This information is critical in our understanding of this case as Clade 2.3.2.1c #avianinfluenza viruses have been endemic in Southeast Asia for ~10 years and human-human transmission ability has not been established. (3/)
As 2022 draws to a close, we’ve been reflecting on some of the highlights (in no particular order) — you can read the full article here: bit.ly/3IfaKYc, or digest the thread below. Wishing you a happy new year and all the best for 2023! 1/23
The #cancer research community has made huge strides leveraging the unique attributes of #nanopore sequencing to characterise cancer at unprecedented resolution, unlocking previously hidden variation and accelerating research to support human health. nanoporetech.com/cancer-research 2/23
In May, @mdelledon took a group of scientists into the Gobi Desert to capture small mammals, including bats, to study their microbiome and they set up a genomics lab in a tent. They demonstrated the utility of the MinION in the harsh, off grid and sandy desert environment! 3/23
Time for the latest @nanopore technology updates. Up next in the auditorium: an Update from the Oxford Nanopore team. #nanoporeconf
Please note, we invite you to read the disclaimer in the slides
CB: More information on Clive’s previous technology updates:
10 minute reminder: @VanessaPorter will be on stage in the auditorium shortly with her talk: 'Identification of novel #genomic structures and regulation patterns at #HPV integration events in cervical #cancer'. #nanoporeconf
VP: HPV is a necessary driver of cervical cancer. HPV integration is present 70% of cervical cancers. Often disrupts E2 gene & causes structural rearrangements. #nanoporeconf
VP: HPV integration often upregulated neighbouring genes. #nanoporeconf
@euanashley's plenary talk: 'The potential of ultra-rapid #nanopore genome sequencing for critical care medicine', will begin in 5 minutes — check out the agenda to find out what else is in store: bit.ly/3M3WlwM #nanoporeconf
@euanashley EA: seeing a $398k car, I recently thought that if luxury cars had dropped in cost as much as sequencing, I could have bought the car for 1c #nanoporeconf
EA: its not enough to have confidence in the genomic data, sometimes we need speed too. #nanoporeconf
GS: Lord Kelvin believed in meaningful measurement to see the whole picture. With nanopore sequencing you gain more comprehensive insights than ever before. #nanoporeconf
GS: In the 3 years since the last time we were at Old Billingsgate, @nanopore has released 200+ products, increased our single-molecule raw read accuracy from 95% to 99.6% & hugely improved our scalability & output. #nanoporeconf
Are you starting your career as an assistant professor and guiding #PhD students for the first time?
Here are a few mentoring tips from the perspective of a current PhD student that may help you.
@AcademicChatter @PhDVoice @PhD_Genie #research @PhDsofIndia
Here are a few mentoring tips from the perspective of a current PhD student that may help you.
@AcademicChatter @PhDVoice @PhD_Genie #research @PhDsofIndia
1) Never keep lab meetings on Monday, Tuesday and weekends. Putting on Monday or Tuesday will force them to work on weekends. Respect the social life of PhD students. It's also good for their mental wellbeing.
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2) Regularly talk about the long term and short term impact that the PhD project is going to produce, like patents, high impact journal papers as well as the societal impact. This will motivate the PhD scholars to work harder, smarter and better.
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Our preprint presenting the #genome of the most #endangered #seabird in Europe #Balearic #shearwater is out in #biorxiv
Cristian Cuevas Caballé @VizuetaJoel @meritxellgeno @SeabirdEcology @RiutortLab @JRozasUB
See 🧵👇 1/7
Cristian Cuevas Caballé @VizuetaJoel @meritxellgeno @SeabirdEcology @RiutortLab @JRozasUB
See 🧵👇 1/7
The Balearic shearwater is a Critically Endangered #IUCNRedlist #seabird endemic of the Balearic Islands affected by #introduced mammals and #bycatch in longline #fisheries. Previous studies predict their extinction by 2070! doi.org/10.1111/1365-2…
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Three steps: (1) Sample Preparation, (2) Data Acquisition and (3) Sequence Data (basecalling)
"[...] everything apart from the computer is designed by Nanopore, but [the computer side] may change in the future, by the way". Unreasonable to think they will build their own silicon specialized for base-calling?
A Thread (🧵)
Let's discuss long-read #sequencing, optical mapping, and the implications of a recent study (linked below).
Please view my disclosures at the end. I've intentionally made this thread more technical as I think it's necessary.
biorxiv.org/content/10.110…
Let's discuss long-read #sequencing, optical mapping, and the implications of a recent study (linked below).
Please view my disclosures at the end. I've intentionally made this thread more technical as I think it's necessary.
biorxiv.org/content/10.110…
First, let's deconstruct the paper's title: "De Novo Assembly of 64 Haplotype-Resolved Human Genomes of Diverse Ancestry and Integrated Analysis of Structural Variation".
De novo (Latin: "Of New") assembly involves sequencing a genome without the help of a reference.
De novo (Latin: "Of New") assembly involves sequencing a genome without the help of a reference.
Assembling a #genome de novo is like solving a jigsaw puzzle without using the picture on the front of the box. You could start with the corners, assemble the edges, and try to fill in the rest using color- or shape-matching methods.
Let me use an analogy.
Let me use an analogy.
Our new method for multiplexing 94 SARS-CoV-2 samples on a #Nanopore #MinION flowcell for £12.72 per sample (extracted RNA to sequencing) biorxiv.org/content/10.110…
It's a simplified lab protocol, which is faster and cheaper, utilising Nextera. We combined it with 96 #Nanopore PCR barcodes, so guppy deplexes out of the box.
We sequenced the same subset of SARS-CoV-2 samples using #Illumina, standard #Nanopore with ligation, and CoronaHiT (48 and 94 samples) with a range of Cts. All raw data in ENA, so useful on its own for comparisons, thanks to @happy_khan
Galru is out today. Its for spoligotyping Mycobacterium #tuberculosis directly from #Nanopore data, and you can get a type from as little as a single read.
Paper: biorxiv.org/cgi/content/sh…
Software: github.com/quadram-instit…
Install: conda install galru
Paper: biorxiv.org/cgi/content/sh…
Software: github.com/quadram-instit…
Install: conda install galru
Its a combined effort with @happy_khan @thanhleviet @timskvortsov Michael Strinden. Galrú is Irish (Gaeilge) for infection in keeping with my recent naming scheme.
One issue I did find was that theres very little #nanopore data for Mtb, which is disappointing since its such an important pathogen (@danybeste & Suzie Hingley-Wilson set me straight on that one)
Brilliant talk by Phill James @Grounded_circus on #SARSCoV2 genome sequencing using @nanopore sequencing. Giving humanity hope in these dark times. Here I will share some information from the talk. Thread.👇
Why #Nanopore for Sars-Cov2 genome sequencing? @nanopore sequencing allows us to do real-time sequencing cost-effectively and with low instrument cost. In the #COVID19 context, it can help us monitor the #coronavirus spread and vaccine efficacy.
.@nanopore was used before for monitoring other viral outbreaks, such as #Ebola: nature.com/articles/natur… and #Zika: genomemedicine.biomedcentral.com/articles/10.11…
