A Most Unfortunate Sequencing Error
If you are in the sequencing business, you'd like to get things right. But sequencing is a form of measurement and measurement has error. No matter how diligent and committed you are, sometimes the data doesn't break your way. Mick Watson has aset of posts and apreprint illustrating quality issues in many deposited bacterial genomes. Some of those are bad luck and some of those are from complacency. Some errors radically affect biological interpretation and some don't. I'm going to detail here one of the worst cases of bad luck I've seen, where relatively small errors sat undetected for ove...
Source: Omics! Omics! - March 21, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Morning Visit to SeqLL
I've written in the past aboutSeqLL, the company which purchased all of the hard assets from Helicos after the latter's demise. At the end of last year, CEO Elizabeth Reczek invited me to stop by for a visit and so I spent a morning having a frank discussion with Dr. Reczek and Director of Sales Lee Dalton and also was treated to a tour of their facilities.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 6, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PromethION: Straining at the Starting Gate
Due to the usual time conflicts, I've only watched bits-and-pieces of the Winter Olympics from South Korea. Which is unfortunate, as I do enjoy observing many of these events as so many combine grace, power and finesse. In the various timed events, the competitors can be seen tightly wound, ready to spring out at the crack of the start. Increasingly, that is how Oxford Nanopore's PromethION looks: a superb performer ready to bolt away.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 25, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT: It Ain't Over'til the Tattoo Wears Off
AGBT officially ended on Thursday night with a space-themed party, but I have a bunch of notes from interviews with company representatives and even a few notes from sessions. So be prepared for a string of further AGBT reports. This dispatch will have some overall thoughts as well as some notes on the possible return of AGBT to Marco Island next year. I also want to mention two good AGBT 2018 summaries, onefrom Dale Yuzuki and another fromDecibio's Stephane Budel.newly appliedRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 18, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT: Twist Biosciences Launches Sequence Capture Product
Twist Biosciences today launched a new product into the sequence capture space. CEO Emily Leproust was presenting to the Gold Sponsor workshop as I started writing this, but she also sat down with me yesterday to preview thenew offering for targeted sequencing.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 14, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT: BioNano Launches New Labeling Approach
AS AGBT opened, optical mapping companyBioNano Genomics announced a new scheme for labeling genomic DNA inputs which substantially improves performance. Sven Bocklandt from the company sat down with me yesterday to walk through the new Direct LabelingRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 14, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT: 10X Previews Three New Single Cell Applications
I spent breakfast with 10X Genomic's Michael Schnall-Levin and two of his 10X colleagues gave me a sneak peak at three new single cell products they are rolling out at the workshop I'm typing away at now. These enable measuring protein targets of antibodies, mapping out accessible chromatin regions withATAC-Seq, and mapping copy number variants (CNVs) at single cell resolution. All use the existing Chromium Controller instrument.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 13, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT 2018: It's Great to Be Back
All sorts of scheduling snafus have kept me away the past three years. So this time around, I vowed to go and made sure my calendar stayed clear. So clear, I forgot to put a reminder down to actuallyregister for the event. Luckily, there were slots still available when I put my flier in.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 12, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT Swag Bag
Today at AGBT is light on the science talks; the afternoon is free for lazing around the resort complex -- or for swimming laps in the lazy river (which makes it a not-so-lazy-river). I can only manage downstream; upstream is an aquatic treadmill. A key task on Day 1 is to pick up one's registration materials. At one conference I failed to do this promptly and discovered to my dismay that the desk wasn't open during the opening reception slash poster session -- so despite being a speaker I had to sneak into the room via a side door! Registering means picking one's meal pass -- I took the temporary tatt...
Source: Omics! Omics! - February 12, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Brown Webcast Note: Corrections and Expansions
After I post something, there's almost always something I realize I left out. In my piece on Clive Brown's webcast of ONT improvements, not only did I forget a few key details but my wording led to some unfortunate confusion, as judged by a comment. Someone took me up on my idea on how detecting large fragments during a run might work -- and showed it doesn't pan out (which Clive Brown confirmed). And to top things off, a BioRxiv preprint showed up that exactly covered something I alluded to.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 10, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
February 2018 Clive Brown Webcast Notes
Clive Brown's webcasts are always entertaining, and even the 6am Eastern Time start for Thursday's didn't hinder that aspect -- though I am thankful I'm not on the U.S. West Coast because I really don't function at 4am. Even at 6am, I was frequently shutting off my iPad screen or exiting the presentation, as screenshots on iOS involve simultaneously pressing Power and Home keys. At that hour, my never great fine motor skills just aren't reliable. Hopefully I won't make the dog's breakfast of this, as that's usually all I'm good for processing at that hour!Still, lots of updat...
Source: Omics! Omics! - February 9, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford Nanopore Outlook 2018
I'm behind on these posts. My usual foibles were largely responsible for a while, but then I had themajor (and sad) family issue that has kept me off balance for two weeks. Someday I may write about that, but for now back to the major sequencing vendors. Though with Oxford Nanopore, the problem is where to start? But now is the time to get moving, both since Oxford's Clive Brown will bewebcasting an update on Thursday and I'll be at AGBT next week and expect to be busy with news flow from that event. Clive's webcast is titled"sub-$1000 human genomes on Nanopore (and other goodies for H1 2018)...
Source: Omics! Omics! - February 7, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Fingerprints on Jupiter
I had hoped to mark my father's 93rd birthday today in my usual way, a call home to exchange well wishes and update him on our goings-on. But two weeks ago he entered the hospital for what turned out to be a final visit, so instead I am writing this.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 30, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio Outlook 2018
Well, I didn't exactly get my Pacific Biosciences preview out beforetheir J.P. Morgan presentation. Luckily, the slides for that primarily projected financials and touted their successes -- and didn't drop any major platform announcements in -- so I didn't miss out. PacBio's position is important and worth reviewing, even if it doesn't change much.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 17, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
iSeq!
Illumina CEO Francis deSouza's J.P. Morgan Presentation did not disappoint. While humdrum financials and touting market dominance and areas of future growth came first, then came the big Firefly announcement (with a name change to iSeq 100) -- and then after another short spell of reviewing the latest Nextera chemistry came a smaller bombshell -- Illumina is partnering with former arch-rival Thermo Fisher (nee Life Technologies nee Applied Biosystems) to move the AmpliSeq multiplex PCR technology over to the Illumina platform.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 9, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
