Discover and read the best of Twitter Threads about #NovaSeq
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Ok, we did try @ParseBio SPLIT-Seq WT kit. We don’t have the data yet but workflow-wise it was super easy. I really liked the simplicity and that the kit comes with pretty much all you need. Totally manageable for anybody who has done 96-well work and multi-channel pipettes. 1/6
They also have a super easy to fill out Excel sheet that makes all the calculations for you. Peace of mind right there. If you counted your cells correctly then you are for a good start. 2/6
You DO need at least 3x more cells input to ensure you end up with the targeted numbers of cells at the end. Of course, viability and cell numbers before and after fixation is critical. 3/6
Oxford @nanopore vs #Illumina #NovaSeq: how far away are they from each other?
I followed with attention the recent PromethION updates, both in terms of new flowcells, with denser pore surfaces, and software and reagents, with the Q20+ basecalling.
I followed with attention the recent PromethION updates, both in terms of new flowcells, with denser pore surfaces, and software and reagents, with the Q20+ basecalling.
It is reasonable to assume that the rollout of the Q20+ updates will be commonplace in the next few months, which means that there is only another decimal in base calling accuracy to put the ONT technology on par with Illumina short-reads. Oxford Nanopore has already announced...
... their work and preliminary results for their updated dual strand base calling, and the modal shows a peak near Q30, which means there wouldn't be much to debate anymore when it comes to per-base accuracy between the two technologies.
I received an email from @NebulaGenomics today, with a discount code for a $299 genome sequencing offer. Which made me wonder: are they using the already cheaper @MGI_BGI #DNBSEQTx sequencing for this? It would mean they can run it at cost or make a small profit from it.
Then you realise there is "analysis" charge on top of the $299 which you can't untick, so the $299 #WGS 30x genome goes up to $499. Still, at $499, you would find it difficult to make money if you were @NebulaGenomics and you were using something like an @illumina #NovaSeq
We are not far away from routinely #genome sequencing every newborn suspected of having a rare/hereditary disorder.
In fact, there will be a point, especially in single-payer health care systems, where it'll be logistically preferable to routinely #genome sequence every newborn.
In fact, there will be a point, especially in single-payer health care systems, where it'll be logistically preferable to routinely #genome sequence every newborn.
What will it take? Management, machines, and money (3M), in that order:
1/ A management system that handles sample collection, carries on the sequencing effectively, and makes the result available: we are not far away from this in, e.g. the UK's (@NHS+Wales/Scotland/NI).
1/ A management system that handles sample collection, carries on the sequencing effectively, and makes the result available: we are not far away from this in, e.g. the UK's (@NHS+Wales/Scotland/NI).
We are much better at this now than, say, 1-2 years ago. See a successful system of coordinating this for lower throughput sequencing but high numbers of samples in #COVID19 cogconsortium.uk
#JPM2021 @carisls My Highlights: in the #CancerDiagnostics area, they position themselves favorably wrt Foundation medicine, Tempus, and Personalis (haven't heard of NEO before). 
They put #LiquidBiopsy at the end of this trajectory slide: (couldn't see any years in milestones for this)
No indication that #Caris are pursuing #Epigenomics profiling of #LiquidBiopsy: they mention exome and transcriptome in their slides.
A petición de @G05Vi les traigo un🧵de tecnologías de secuenciación de ADN y cómo han servido para caracterizar al #SARSCoV2
(Contexto:soy investigador de la UNAM, experto en Genómica y Bioinformática. Del 2020 a la fecha dedico mucho tiempo al estudio del #SARSCoV2 y #COVID19)
(Contexto:soy investigador de la UNAM, experto en Genómica y Bioinformática. Del 2020 a la fecha dedico mucho tiempo al estudio del #SARSCoV2 y #COVID19)
1/El ADN (Ácido Desoxirribonucleico) es una molécula que se en todos los organismos biológicos. Su importancia es que en dicha molécula reside toda la información genética de dichos organismos. Básicamente el ADN es el manual que tiene todas las instrucciones de funcionamiento 🧬
2/A finales de 1800s, Friedrich Miescher, un médico/biólogo suizo fue el primero en aislsar ácidos nucleicos q los cuales llamó nucleina. Desde entonces la ciencia ha avanzado mucho, pero no quiero entrar mucho en la historia del ADN sino en como se "lee" y que info nos da
Drawing Innovation: @illumina Super-Resolution Optics
Recently, $ILMN unveiled the NextSeq 2000, a mid-throughput sequencer w/ a ~2X reduction in operating costs ($/GB).
We think the upgrades inside the NextSeq 2000 may soon enable a $100 clinical-depth human #genome.
But how?
Recently, $ILMN unveiled the NextSeq 2000, a mid-throughput sequencer w/ a ~2X reduction in operating costs ($/GB).
We think the upgrades inside the NextSeq 2000 may soon enable a $100 clinical-depth human #genome.
But how?
The cost savings come from (1) a new upfront #chemistry and (2) super-resolution optics. We think @illumina will use real-world customer data on the NextSeq 2000 to optimize 1 and 2, then possibly upgrade the #NovaSeq line.
illumina.com/systems/sequen…
illumina.com/systems/sequen…
I'm going to briefly (!) illustrate how #sequencing (*by synthesis*) works, walk through a farming analogy, then dive into some technical details. (Sources at the end)
Below is a general overview of a whole genome sequencing workflow (sample in, data out).
Below is a general overview of a whole genome sequencing workflow (sample in, data out).
