Ultima Genomics Storms Out Of Stealth Promising $1/Gigabase Short Reads
To date, the new entrants targeting Illumina ’s short read business have been aiming at the middle of Illumina’s range, trying to take on NextSeq. Element Biosciences is touting high accuracy for a low price.  Omniome (now PacBio) alsohas positioned itself to tout accuracy.  Singular Genomics is claiming to enable great flexibility and fast runs. But all aimed at NextSeq. As part of the run up to AGBT another company is decloaking from stealth mode: Ultima Genomics, however they are going not after NextSeq but full throttle after Illumina’s pinnacle, the NovaSe q running the S4 flowcell. The value proposit...
Source: Omics! Omics! - May 31, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
London Calling 2022: Peptide Sequencing
London Calling was last week and Clive Brown's big revelation was a peek at Oxford Nanopore's progress on enabling peptide sequencing on the platform.  Peptide sequencing and identification is a hot area right now, with multiple startups looking to provide alternatives to mass spectrometry approaches. Clive stressed that the technology is very early in development. It's definitely a clever fork of the existing DNA sequencing technology.  However, it also illustrates a significant organizational challenge which Oxford. So I'm going to spend a post focused on this while I figure out how to slice up th...
Source: Omics! Omics! - May 23, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore Knights' Notes
Clive Brown gave a"mezzanine" update on Oxford Nanopore just over two weeks ago titled"The Knights Who Say Me".  Clive reiterated a lot of prior guidance but did make a few announcements that are relevant to the ongoing history of the Oxford Nanopore platform - and blessedly, he omitted for time's sake a deep coverage of that history or the usual Nanopore 101 tutorial.   In particular, two long-time components of the platform are now headed for the exits.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - April 15, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
The End of the Beginning of Human Genome Sequencing?
Today inScience a slew of papers have been published from the Telomere-to-Telomere (T2T) Consortium. The flagship paper details the generation of a complete genome assembly from a Complete Hydatiform Mole (CHM) cell line which is telomere-to-telomere for all 22 autosomes plus X (assembly T2T-CHM13); the compani on papers apply this groundbreaking assembly to a number of biological questions. PacBio CSO Jonas Korlach and I chatted yesterday about the PacBio contribution to the flagship as well as two of the other papers, as well as another T2Tpreprint on automated assembly anda related paper from Heng Li and colleagues...
Source: Omics! Omics! - March 31, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Using R to detect the pressure wave from the 2022 Hunga Tonga eruption in personal weather station data
It seems like an age ago, but in fact it was only mid-January 2022 when this happened:
The satellite imagery from the Hunga Tonga eruption is unreal. Direct your attention to the lower right. The eruption then shock wave is simply incredible. pic.twitter.com/OTLCgyEozQ— Taylor Trogdon (@TTrogdon) January 15, 2022
Wow. Now, pause for a moment and try to recall the last time you read any news about Tonga since the event.The eruption sent an atmospheric pressure wave, clearly visible in this imagery, around the world. Friends online reported that this was detected by their personal weather stations (PWS) which made ...
Source: What You're Doing Is Rather Desperate - March 29, 2022 Category: Bioinformatics Authors: nsaunders Tags: australia environment statistics world news hunga tonga rstats weather wunderground Source Type: blogs
Using R/fitzRoy to ask: how many times a V/AFL team with the same lineup has played together?
If you sit in the intersection of “likes Australian Rules football / finds sport statistics interesting / is on Twitter”, you’ve probably come across Swamp. One of his recent tweets tells us that:
No V/@AFL premiership winning lineup have all played together in another V/@AFL match, there has always been at least one person missingAll MELB 2021 premiership players are still at the club in 2022 @melbournefc— Swamp (@sirswampthing) March 16, 2022
You may go on to ask: has any team lineup from one of the almost 16 000 recorded games played together again in another game? And if so, how often?
Th...
Source: What You're Doing Is Rather Desperate - March 28, 2022 Category: Bioinformatics Authors: nsaunders Tags: australia sport statistics afl fitzroy rstats Source Type: blogs
Element Unveils AVITI
Element Biosciences is launching their AVITI sequencing system today in a blitz of events.  At February’s end they flew me out to visit their San Diego facility and gave me quite amazing access to senior staff, Board of Directors members for an entire day of discussions. They even videotaped me! Many of those discussions got deep into technical weeds in a most enjoyable manner.  But for those wishing to jump straight to key details, AVITI is a desktop instrument priced at $289K, a bit below NextSeq 2000, which can run two flowcells entirely independently; two sequencers for the space and outlay of one. At a cost o...
Source: Omics! Omics! - March 14, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Pro Tip: Customer Hostile is Never A Good Look
A bizarre incident happened on Twitter yesterday.  Someone contemplating using Oxford Nanopore to sequence a large, complex genome on a tight budget was asking technical questions about whether to optimize their libraries for overall yield or long inserts, and was getting useful advice from some of the top academic scientists who have propelled O NT forward. One of them suggested using Circulomics products, and that was followed by an ominous yet vague warning from an ONT employee. But not just any ONT employee, but Chief Strategy Officer Spike Willcocks. Having not seen a retraction of that tweet, I'm here to ...
Source: Omics! Omics! - February 17, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Parse Bio Pools Further Funding
Seattle-based single cell analysis firm Parse Bio is announcing this morning a $41.5M Series B round of funding, pushing their total raise just over $50M.  Parse uses chemical fixation to lock biomolecules onto their enclosing cells or nuclei, which can then be manipulated without releasing their contents. This enables a series of split-label-pool operations to tag the molecules of interest with barcodes so that in the end each cell has a unique b arcode. The protocol requires no specialized instrument, enables collecting samples over different timepoints while quenching changes in gene expression and can scale to ve...
Source: Omics! Omics! - February 15, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Notes from a Conversation with PacBio's Christian Henry
PacBio CEO Christian Henry was kind enough to chat with me by videoconference just after JP Morgan.  To get the the obvious issue out of the way, let me say that while it is common to agree to meet with interview subjects at some future date when they are in Boston, he is the first one to suggest he would just stop by my desk and we'd head to a break room.  Henry sits on my employer's board, so if you think that shades my opinions you are forewarned.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 31, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Could Hercule Poirot Crack The Case of Genapsys' Business Strategy?
If you love a good mystery, let me try to draw you in to the enigma of Genapsys' business strategy.  Genapsys presented last week at J.P. Morgan, but nobody who wasn't there knows what they said or presented.  Keeping their future plans hush-hush is a strange course for a company that hasn't caught fire and is about to face multiple well-funded new competition.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 17, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Illumina Teases Two Glittering Enigmas
Illumina's J.P. Morgan presentation was largely focused on various applications of their platform.  But on the further platform development side, they did throw out two new products as very, very limited descriptions: Chemistry X as the future of sequencing-by-synthesis and Infinity for 10 kilobase synthetic reads. Both have triggered a lot of speculation and indeed some very clever sleuthing , since neither really had anything but the faintest of details providedRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 12, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Apologies & A Vow To Do Better
To my readers: I am quite embarrassed by the multiple errors which were present in the first two postings of the year, which include incomplete sentences in jumbled paragraphs, small but key errors of fact and writing"short read" in a key place where I meant"long read'. They are the sort of errors I can be quite harsh on others making.  I put too much emphasis on pushing these out and far, far too little on proofreading and reviewing them. You deserve better.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 11, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Three Reactions from December's PacBio+Invitae Mendelspod
Theral Timpson hosted PacBio CEO Christian Henry and Invitae CEO Sean George for aMendelspod podcast back on Pearl Harbor day last month. It's a fun, chatty interview with the two which illustrated why these two companies have an excellent strategic fit. I won't summarize all of it, but I did have strong reactions to three pointsRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 6, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2022: A Wild Year for Short Reads?
It looks like 2022 might be an exciting year for the short read genomics market, with new players taking on Illumina.  J.P. Morgan will be virtual next week, so perhaps some of the players will make some announcements. Here's some thoughts on the situation as it stands now in a space where many of failed before -- QIAGEN, ThermoFisher (SOLiD) and Roche(454) -- as well as some have bailed out before even entering -- Agilent.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 3, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
