In #NextGenerationSequencing news, $ILMN Illumina has some more details on the website for the NextSeq 1000/2000 kits, now including a 100 cycle kit for the P1 flowcells, and the 600 cycle kits for P1 and P2. Image
The interesting detail is that the P2 600 cycles kit gives 300M Reads CPF (Clusters passing filter), compared to the equivalent 300 cycle kit on the same flowcell (400M). So either the diameter of the wells is different, or about 100M Clusters are "lost" in the 600 cycle kit.
If the diameter of the wells is larger in the 600 cycle kit, this should allow for larger inserts, which would then benefit from being sequenced longer from both ends. This would make sense to me, but it requires manufacturing a different flowcell.
If the diameter of the wells is the same as the 300 cycle kit, then many of the inserts may land on adjacent wells while growing via ExAmp (or afterwards), thus increasing the number of duplicates and/or the number of non-clonal wells. Also, it could bias the sequencing of the
inserts towards the shorter ones, as the longer inserts would be more prone to jumping out of their original well.

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More from @AlbertVilella

Feb 25
As we see videos in social media of the first $PACB PacBio Revio to enter the @broadinstitute , with the promise of the long-read $1000/genome in place, what does it look like today to set up a Next-Generation Sequencing factory/institute?
There have been many of these institutes come and go, and probably the @broadinstitute (Cambridge, US) and the @sangerinstitute (Cambridge, UK) are the two referents in historical terms and in their magnitude of achievements in #genomics. So if we take them as an example, what do
we learn from them?
1) They were successful at being early adopters of large-scale Sanger Sequencing.
2) They were very well funded from the get-go, and contributed in large part to the success of sequencing the reference #human #genome in 2000-2001.
Read 46 tweets
Feb 24
One of the rather big announcements by $BLI Berkeley Lights (soon to be renamed PhenomeX) is that there would be a new Beacon instrument released in 2023: the Beacon Quest, a 2-chip optofluidic system for academic research. Image
Those of you that have been reading this account for a while will remember that the Beacon is a multi-million dollar large-fridge/freezer instrument that does high-throughput single-cell phenotyping, and the main product in the product line for Berkeley Lights (PhenomeX).
The main perceived attraction of the instrument is that it allows for the "functional assay" to happen in single-cell manner, so the selection of cells can happen for the intended function that they were screened in the first place.
Read 5 tweets
Feb 11
The world of Next-Generation Sequencing (NGS) post-#AGBT23:
1) Some will say that $ILMN Illumina is sleep-walking into a cliff: the company has been dominating the field with 80-90%+ of the market-share, but they are unable to retain their technological advantage to competitors:
- Illumina doesn't have the most affordable $/Gb platform anymore, currently at $3.2/Gb, and $2/Gb in H2 2023, but others are already at $2/Gb, $1.5/Gb and will be at $1/Gb in Q3 2023.
- Illumina doesn't have the longest read technology, or anything near the competition in terms of read length times $/Gb. Oxford @nanopore is unmatched with their ultra-long read technology and is nearing $10/Gb Q30+ performance, as is PacBio on 15-10Kb reads.
Read 21 tweets
Feb 10
A summary of announcements/highlights from #AGBT23 (in no particular order):
#AGBT23 cfDNA methylation profiling as a blood biomarker for Congestive Heart Failure. This is from the same team that gave you the @GrailBio Methylation Atlas, now applied to biomarker discovery.…
#AGBT23 Miga on the comparison between PacBio Revio and Oxford @nanopore High Duplex / UltraLong reads. PacBio 21/46 T2T and ONT 24/46 (higher is better). Ultralong reads scaffolding for both (unconfirmed) would mean ONT lead is even bigger.
Read 13 tweets
Feb 10
In #NextGenerationProteomics news, today we cover the basics of Proximity ligation assay (PLA) technology, also known as proximity barcoding assay technology, which is a method for detecting protein-protein interactions in cells or tissues.
The assay is based on the principle of ligating two probes (such as antibodies) that are in close proximity to each other, typically within a few nanometers. The ligation reaction produces a circular DNA molecule that is amplified by polymerase chain reaction (PCR) and
can be detected by sequencing or by fluorescence-based microarray readouts. The technology allows for the quantification of specific protein interactions in complex biological samples and can be used for a variety of applications, including drug discovery,
Read 18 tweets
Feb 9
#AGBT23 More details on the $ILMN Illumina Infinity reads technology from Alex Aravanis (post from LinkedIn).
Also first data shared on XLEAP-SBS chemistry for the NextSeq 1000/2000 instruments. Not sure why would anyone buy one of these instruments given the alternatives from @ElemBio and @CompleteGenomic 's G400.
First shipment on NovaSeq X: if Illumina can beat the competition at anything in the next few months, it'll be on manufacturing and deployment of the NovaSeq X.
Read 4 tweets

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