Is Illumina Delivering the MVP of Long Reads?
At AGBT last week Illumina released additional details on their still incubating Complete Long Reads (CLR) product (formerly known as Infinity) but is still holding back both some interesting technical information as well as exact performance specifications. Illumina is already floating some of their marketing messages, which in some cases are dependent on some of those still-in-flux specifications and some of the claims may not withstand careful scrutiny. And Illumina continues to make statements that irritate anyone with deep technical knowledge of the long read space. The reaction by attendees was definitely mixe...
Source: Omics! Omics! - February 21, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
What's AGBT Like?
AGBT begins in less than 24 hours, and the signs are everywhere here at the Diplomat Resort in Hollywood Florida. I arrived Friday with family, and the count of old friends I've chatted with is steadily climbing. If you somehow forgot about the meeting, the insides of the elevator doors will remind you. This is the fifth time I've attended in person, plus heavy monitoring of about twice as many via Twitter. It's one of the premier events of the genomics conference schedule, and if you haven't been it's certainly fair to ask why? Or whether you would want to go to a future edition? So I'...
Source: Omics! Omics! - February 5, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT 2023 Is Nearly Upon Us!
AGBT is less than a week away in Hollywood Florida - and I've been letting everything else get ahead of writing anything here. The JP Morgan Conference at the beginning of this month didn't have major fireworks from the sequencing vendors, but did have some news.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 31, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Has your knowledge stopped updating?
Some years ago I read an article – I forget where – describing how our general knowledge often becomes frozen in time. Asked to name the tallest building in the world you confidently proclaim “the Sears Tower!”, because for most of your childhood that was the case – never mind that the record was surpassed long ago and it isn’t even called the Sears Tower anymore. From memory the example in the article was of a middle-aged speaker who constantly referred to a figure of 4 billion for the human population – again, because that’s what he learned in school and had never mentally ...
Source: What You're Doing Is Rather Desperate - January 27, 2023 Category: Bioinformatics Authors: nsaunders Tags: education R statistics readr read_csv rstats tidyverse Source Type: blogs
Editing metadata in trail camera images using R, magick and exiftool
I have a new hobby: camera traps, also known as trail cameras. Strapped to trees in my local bushland they sit in wait, firing automatically when triggered by a passing animal. Once in a while, something quite magical happens.
The camera model I chose is the Campark T85 which for me, had the right combination of features and price point. One useful feature is the ability to transfer images and video to a phone wirelessly (albeit through a rather clunky phone app). Unfortunately, images retrieved in this way have one major flaw: an almost-complete absence of metadata. There is no GPS in the camera of course, but th...
Source: What You're Doing Is Rather Desperate - October 25, 2022 Category: Bioinformatics Authors: nsaunders Tags: environment programming statistics campark exiftool metadata photography rstats trail camera Source Type: blogs
PacBio Revio: Same Footprint, 80% The Time, 15X The HiFi!
PacBio has been rolling out announcements around the ASHG meeting and now delivers a huge one: the next generation SMRT instrument “Revio” will roll out next spring and it’s a big step up in throughput. With Revio’s 15X boost in per-run throughput over Sequel IIe, PacBio is touting this as 30X HIFi genomes for under $1K sequencing consumables per genome. Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 25, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Better Than FizzBuzz: First Bioinformatics Problem in an Erratic Series of Indeterminant Length
Periodically in my work or during writing this blog I come across computational problems that have the aspects of making, at least in my mind, very good teaching problems. Some of the characteristics are that the basic problem is relatively simple to explain, the skills required are reusable on other problems, the concepts are germane to other problems and that the posed problem can be expanded in steps to something much richer. Such problems might even be the nu cleus of undergraduate or even high school bioinformatics projects, though with the recent news of a high schooler sequencing his dead pet angelfish's ge...
Source: Omics! Omics! - October 19, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
General Inception Aims to Ignite New Company Formation
A week ago, a company calling itself General Inception emerged from stealth as a new concept, which they call an “Igniter company”, to promote the formation of new life sciences company. As described to me in a phone conversation with General Inception CEO Paul Conley, General Inception provides a range of science and business expertise and support to enable embryonic ideas to condense into functional st artups. The igniter metaphor Conley offered me is the spark plug of a car: it is required to start the engine and continues to provide a key part of the functioning whole. Conley extended this to say that Gener...
Source: Omics! Omics! - October 6, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
What Conversation Does Each Sequencing Instrument Vendor Wish You To Have?
Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 5, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Illumina Roadmap Part 2: Infinity Becomes Illumina Complete Long Reads
The Only Thing Clear About Infinity Is It Is Now Complete Long Reads. Illumina told us a new name for Infinity -- Illumina Complete Long Reads -- and an initial pair of products, but didn't reveal anything new about the underlying tech. They threw out a number of claims, but very vague ones. Particularly confusing is that it"isn't synthetic reads". If not, then what is it? Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 3, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Illumina Roadmap Part 1: NovaSeq Xplus & XLEAP-SBS Chemistry
Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 2, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Notes From Coffee With MGI
A couple of weeks ago I sat down for coffee with a pair of MGI representatives - American Region CEO Yongwei Zhang and Director, Global Business Development Damon Zhang. Since I hadn’t been at AGBT 2022 (my 2023 application already filed!). Yongwei and I had planned to try to catch up the next time he was in Boston area, so I braved our current subway issues (not one, but two major lines shut for extended maintenance!) and covered a range of topics.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - September 21, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
SRA Entries Should Not Ever Disappear Into Thin Air
I ran into an annoying problem last night and was quite steamed, but had the discipline to wait until morning to vent publicly about it. Now I'm more in a morose mood on the subject, not furious but still quite frustrated. The quick version of what happened is I'm belatedly trying to go through some nicely documented reproducible analysis code to explore some concerns I have with the analysis, and the code is working on an SRA entry -- and that SRA entry is the entire point of the analysis. And that SRA entry which I know once existed now doesn't - other than this code and the preprint to go with it, it'...
Source: Omics! Omics! - August 23, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Supply Stall Slows Singular
Singular Genomics reported earnings last week and delivered an unpleasant surprise: inability of suppliers to make timely deliveries of key (but unspecified) hardware components have slowed G4 instrument production to a very slow crawl. Given the lively competition in the desktop short read space, this is a serious setback for Singular's commercial launch. Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - August 16, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT 2022: Overhanging Questions
AGBT broke up a couple of weeks ago and I've failed to write anything here so far. It was frustrating not attending, but not registering for a meeting in February seemed prudent given the pattern of COVID waves - I hadn't considered (nor would have wanted to bank on) AGBT organizers reacting so well and rescheduling the meeting. It sounds like a number of attendees did catch the virus at the meeting -- though I'm presumably still quite protected by my infection a month earlier. Anyways, I'm going to organize this around one to two questions that hover in my head for the different sequencing provide...
Source: Omics! Omics! - June 23, 2022 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
