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
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
Reflecting on Anniversaries and Changes
As the year closes out for me (as I write this, it may well have closed out for some of you!) I'm reflecting on some anniversaries that were concentrated in this year, particularly those that are multiples of an early evolutionary developmental decision millions of years ago.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 31, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
ONT Community Meeting 2021
Oxford Nanopore held their annual Community Meeting online at the beginning of this month.  As is typical for this stage of the ONT news cycle, most topics were confirmations and updates of earlier projections, with little brand new material. There was one surprise, a new concept for running nanopore with little to no auxiliary lab equipment. Oh, and perhaps in the surprise category is Oxford appears to be finally moving away from the R9 pore which has been their mainstay for many years now.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 13, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Look at Two HiFi Polisher Preprints
PacBio has made its reputation delivering very high accuracy long reads, which they have branded HiFi. These are based on their circular consensus technology: each template DNA molecule is converted into a single continuous circle of DNA which can be read in a rolling circle reaction. Â The"movie" is converted to raw base calls and the adapters are clipped out, leaving"subreads" which can be aligned together to generate a consensus (CCS) read. Â With many passes over the same molecule and its complement, the relatively high (~15%) error rate of the raw data can be brought down substantially using an H...
Source: Omics! Omics! - October 26, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio Pulls Down Circulomics
I was on vacation early this week when the news broke that PacBio has acquired HMW DNA solid phase extraction kit maker Circulomics -- the kind of vacation that I need where the scenery is gorgeous and the internet access terrible.  Where solid phase means monumental slabs of granite with diabase intrusions being attacked by a high salt liquid phase. Where I actually sighted Atlantic Puffins and didn't once think about sequencing their genomes ('til now!).  But now I'm back to work and genomics.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - August 4, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio Enters a Binding Agreement to Acquire Omniome
Pacific Biosciences announced today that they are slurping up short read sequencer startup Omniome for around $800M.  Omniome has been developing an interesting clonal read technology. On the conflict-of-interest side, many years ago (and I think an entire management team different) Omniome treated myself and my family to a weekend in San Diego (it was my son's birthday weekend) so I could look at their technology back then -- my NDA has expired but so has most of my memory of what I saw at that meeting!  Also the periodic reminder that PacBio Christian Henry sits on the board of my employer, though we haven'...
Source: Omics! Omics! - July 20, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
