A Short Master Class in Benchmarking
There's ablog post on BioJulia.netthat is well worth reading, even if you don't use Julia or I'd argue if you don't actually program. It looks at an issue of performance that was raised with BioJulia and with fierce but respectful passion examines the critique and explores just why BioJulia didn't perform well in the comparison. In the end, this triggers a code review and a huge speed increase in the problematic areas -- which will widely benefit BioJulia users.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 12, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Sampling Current & Future Directions in PCR Diagnostics
My qPCR explainer seems to have done relatively well, though it took some refinement after readers caught a number of errors. The most embarrassing of those is that I got my PCR ramp units upside down, so instead of 4 seconds or so per degree C it's degrees C per second so my times were off by a factor of16!Ouch! Despite that miscue, I'm here going to explore some of the variants on PCR that are out there, including some that are being employed searching for the newly renamed COVID-19 virus. Included here are some of my own speculations and musings, so as always remember I'm someone who thinks about th...
Source: Omics! Omics! - February 10, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A qPCR (aka RT-PCR aka rRT-PCR) Explainer
I've gotten in a number of Twitter threads and seen a lot of Quora questions about the qPCR test for the Wuhan coronavirus that I realized would really be best handled by writing an explainer. I'm intending it for financial types, reporters and anyone from the lay public interested in learning a bit more. For most regular readers of this blog, there won't be anything new to you. If you'd check me for accuracy, I'd be grateful but perhaps many will skip over this one. That also means I going to try to resist my usual urges to make lighthearted references to popular culture; they're a good...
Source: Omics! Omics! - January 31, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Can ONT Maintain Grip on Burgeoning Flowcell Herd?
A notion dawned on me when I was mentally planningmy write-up of the Nanopore Community Meeting, but I decided to put off fleshing it out until a later date. After a bit of procrastination plus a crush of other ideas, here it is: Oxford Nanopore flowcell lineup has been a bit complicated for a while, but it's probably going to get worse. There's always been serious issues with the current level of complexity and it's hard to believe this will do anything but escalate.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 29, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
An Ultimately Tufnellian Look At Oxford Nanopore R10.0 Homopolymer Performance
Homopolymeric sequences have never been easy for any sequencing platform, but single molecule sequencers struggle the most with this. Oxford Nanopore has made remarkable strides in both raw an consensus accuracy via chemistry and software improvements, but still is challenged by systematic problems with homopolymers. The R10 series of pores is intended to significantly improve performance by having a longer narrow region to i nteract with more bases, and at the Nanopore Community Meeting there were several slides touting improved performance. Nanopore's slides have an X-axis that goes to 8. By happy circumsta...
Source: Omics! Omics! - January 26, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
An Ultimately Tuftnellian Look At Oxford Nanopore R10.0 Homopolymer Performance
Homopolymeric sequences have never been easy for any sequencing platform, but single molecule sequencers struggle the most with this. Oxford Nanopore has made remarkable strides in both raw an consensus accuracy via chemistry and software improvements, but still is challenged by systematic problems with homopolymers. The R10 series of pores is intended to significantly improve performance by having a longer narrow region to i nteract with more bases, and at the Nanopore Community Meeting there were several slides touting improved performance. Nanopore's slides have an X-axis that goes to 8. By happy circumsta...
Source: Omics! Omics! - January 26, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
UST Bets on TELL-Seq
I've made a few references recently to TELL-Seq, both inmy flawed analysis of BioNano Genomics (I missed a key business development in their raising $18M in October; I stand by the science comments and fear that the fund raise buys them about a year of time) and on10X Genomics discontinuing their genome assay kits. Now to actually dig into that technology -- a bit late given thepreprint came out last fall, but better late than never. So put on yoursunglasses and hoodies, conjure up the image of early television chefs and key up thetheme music for The Lone Ranger, because here I go.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 25, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Can BioNano Genomics Map A Way Past Twin Perils?
When playing with the structure of this piece in my mind, it occurred to me that Norman Maclean'sthoughts about fly fishing apply just as well to biotechnology companiesIt is also interesting that thoughts about fishing are often carried on in dialogue form where Hope and Fear -- or, many times, two Fears -- try to outweigh each otherThe executive team atBioNano Genomics may well be gripped by this situation, as they are faced with two great perils: their finances and their markets.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 22, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Genia: It's Alive!
Once in a while I get the thrill of someone sending me a really good tip - that surge that comes with knowing that I know something that most people don't. That rush of knowing that soon I'll get to spill the beans. It's great, even if it upends my widely disseminated opinions. Even if a moment later I realize that if I had thought harder I would have unearthed the nugget on my own. All of which is the case here -- my tea leaf reading thatRoche partnering with Illumina on diagnosticsindicated that Genia is no more -- well, that interpretation is no more. Because I got a hot and verifiable tip that...
Source: Omics! Omics! - January 21, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
10X Genomics Exits Genomes
10X Genomics original product was a kit for generating linked reads from genomic DNA. The idea had been kicking around for a while, partitioning long DNA into compartments and generating tagged libraries from each compartment. This enabled both genome assembly and haplotyping from very small amounts of DNA. When first reviewing 10X's slides from J.P. Morgan I had this thought"where's the genome kits" but then forgot to include it in my write-up. Now I'm even more chagrined to discover that the explanation had been posted days before the conference: 10X has told their customers that their gen...
Source: Omics! Omics! - January 18, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
JPM20 Loose Ends: Agilent, ThermoFisher, 10X Genomics, NanoString - plus PacBio & ONT
Time to close out J.P. Morgan season with a grab bag of kvetches and kibbitzing on multiple'omics companies that presented. Much of this has been stimulated by Twitter discussions, with particular credit going to Varro Analytics and Albert Vilella. While I've never been to J.P. Morgan physically and am skeptical I'll ever go, reviewing all this is a great prep for AGBT -- which I'm happy to be returning to this year for it's last Marco Island appearance for many years (forever?).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 16, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Bold Genapsys Talk at JPM20
Genapsys' CEO Hesaam Esfandyarpour presented today at the JPM Morgan Conference and delivered an expansive vision of where the company is going both this year an the long term. This includes planned commercial launch of the 144M chip this year, an aggressive expansion into international markets and another round of"pre-IPO" financing.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 13, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
JPM20: Illumina Launches Super Resolution Instruments
Illumina presented this morning at the J.P. Morgan Healthcare Conference (presentation,slides&breakout). For us sequencing geeks, the biggest news is the launch of a pair of new sequencers -- but not where either myself or Shawn Baker anticipated. Rather than doing something about the low end of their line (as I predicted) or replacing the MiSeq asShawn guessed, Illumina perceived a need for desktop instruments to span the range between the existing NextSeq 550 and the NovaSeq and has christened the new instruments NextSeq 1000 and NextSeq 2000. They also come with some slick new technologies embedded.Read more...
Source: Omics! Omics! - January 12, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
JPM20: Roche Links with Illumina On Diagnostics
Another bit of Illumina news released at J.P. Morgan today is thatRoche Diagnostics is partnering with Illumina. The 15 year partnership (same duration as with QIAGEN) will place Roche diagnostic assays on Illumina clinical-grade sequencers as well as the two will jointly work for regulatory approval of Illumina's TruSight Oncology assays. Roche has extensive experience in oncology, particularly since they own Foundation Medicine. This suggests that Roche is happy with a two pronged strategy in oncology diagnostics, selling assays on their own through the partnership while their Foundation arm offers an all-in ser...
Source: Omics! Omics! - January 12, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Is Illumina Vulnerable At The Bottom?
According to both the FTC and CMA, Illumina holds a nearly complete monopoly on the sequencing market, with other players (Ion Torrent, Oxford Nanopore) holding on to toehold niches. Illumina has held that position for an extended period, so what might upset it? I'm going to explore the case that they may have some serious inroads at the bottom of their line.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 11, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
