More from @AlbertVilella

Albert Vilella

@AlbertVilella

Apr 8

@nanopore

Reviewing the Oxford @nanopore presentation now available to replay. Two highlights/thoughts that I didn't tweet about before:
1) Spike-in for re-training
2) Strand-specific DNA modifications

1) Looking at the kind of stuff presented, where temperature settings, salt, etc. are being more available to end-users, there is an opportunity here to retrain models and improve basecalling for specific datasets.

On a much simpler level, Illumina sequencer did and still do some of that: one would need to spike-in a certain amount of PhiX for the machine to calibrate itself. For low-complexity applications, like 16S sequencing, this could be as high as 25-50% of the reads/throughput.

Read 12 tweets

Albert Vilella

@AlbertVilella

Mar 19

@ElemBio

Recap on #NGS after the @ElemBio #AVITI instrument release. Who are the main players in NGS?

Illumina remains the market leader with the short-read SBS technology. They segment their products into high-throughput (NovaSeq $1M), mid-throughput (NextSeq $220-350K) and low-throughput (MiSeq, MiniSeq, iSeq $40-150K).

Then there are to large players, but smaller to Illumina in comparison, in the long-reads field: Oxford Nanopore, with their MinION, PromethION and other modes of sequencing, and PacBio, with their Sequel2 instrument, but with a future play on short-reads with Omnione.

Read 18 tweets

Albert Vilella

@AlbertVilella

Mar 14

@elembio

Element Bio (@elembio) is announcing their first instrument today. I'll concentrate on my own highlights on the presentation, which I am sure it'll be available as a video later on.

My professional interest on the announcement today is: could this be a replacement to a mid-throughput instrument like the NextSeq 2000/1000? If the price in the first specs slide is right, I think the answer is yes!

The Challenge -- Decrease Cost/Gbp without requiring ultra-high throughput

Read 30 tweets

Albert Vilella

@AlbertVilella

Feb 20

@10xGenomics

Quick history of @10xGenomics products:

=== Linked-Reads Chromium Genome and Exome ===
10x Genomics started as a company by selling instruments and reagents for their Linked-Reads method to generate long synthetic DNA reads out of short-read readouts such as those from Illumina SBS sequencers.

These Linked-Reads were useful for de novo genome assembly applications, where the length of the reads is crucial to produce long assembled sequences. As of June 30, 2020, the company discontinued the sale of the Chromium Genome and Exome product lines.

Read 13 tweets

Albert Vilella

@AlbertVilella

Jan 23

Those who follow my account for a while will already know that I've been following the field of Next Generation Sequencing for many years now, and I keep a series of resources comparing different platforms and technologies.

Beyond the first tier of 4-5 large NGS companies out there, such as Illumina, PacBio, Oxford Nanopore, Thermo's Ion Torrents and MGI Tech, there is now a growing group of small companies pinning for an NGS market which is growing and maturing in many ways.

I keep a table comparing these companies, with around 40 different ones, although some of them have a small chance of making it into the market, and they may be acquired by someone else to expand their technological capabilities. bit.ly/nngseq

Read 10 tweets