Friday, February 17, 2017

#AGBT17 Tweet Archive is Up!

I've used my scheme for collecting and organizing tweets to capture most of the feed from this week's AGBT17 conference.  I still need to pore over these in detail, so I won't try to distill out much thoughts (other than single-cell sequencing is clearly in exponential growth phase!).

Monday, February 13, 2017

Bagging Novel Enzymes Via Mass Spec Metabolomics

Obtaining a complete genome sequence for a bacterium or archean is essentially a solved problem, if you can culture the bug.  Grow up biomass, purify the DNA and then use PacBio alone or a combination of long reads (PacBio or Oxford Nanopore) and short reads.  These should yield a closed genome with a very low error rate.  A few bugs spit at you by repeated failing PacBio sequencing or having some monster prophage or other repeat that is longer than the read lengths, but these are very rare.  With advances in metagenomics techniques, the solving of uncultured genomes is becoming increasingly easy and many of these remarks also apply to fungi and other eukaryotic microorganisms. Once you have the sequence, then the lack of introns in bacteria and archea makes gene prediction almost trivial, and you now have a parts list for the organism.  But is that a useful parts list?  A new paper in Nature Methods makes some progress in improving the utility of those parts lists, though we are still far from actually fully understanding an organism given its genome.

Thursday, February 02, 2017

Could Hermione Tackle MinION Yield Variability?

A bit of a foray into Oxford Nanopore land again.  By replacing a bench bumbler with someone competent, we've seen some success with our MinION at Starbase.  Highly variable yields though.  I've done some looking and discovered this isn't a unique experience.  And now Oxford is suggesting that software upgrades alone will give MinION about another 50% boost in yield; it will be interesting to see what this does for variability.  Finally, I have a notion of some of the sources of variability and an idea for a troubleshooting tool

Wednesday, February 01, 2017

Illumina Drops NeoPrep

At the 2015 AGBT meeting, Illumina launched the NeoPrep, a ~$40K instrument to automate the preparation of up to 16 sequencing libraries at a time, using a technology called electrowetting microfludics. Now news comes that Illumina is dropping the NeoPrep, halting sales immediately and allowing existing users about a year of reagents.  What happened and how does it impact genomics?

Tuesday, January 31, 2017

On The International Nature of American Biotech

I'll spend two hours in project meetings tomorrow. Around the table will be a group of scientists who are all at the top of the game and among the best in the world at what they do. We will be trying to push forward new antibiotics to save lives. Yes, we are also trying to be rewarded monetarily with it, but we all share a mission to improve humanity by finding new drugs for important medical needs.

Friday, January 27, 2017

Perl: The Bad Habit I Can't Quite Kick

TULIP is a new assembler for long, error-rich reads such as from nanopore. I was a bit stunned to see that TULIP is written in Perl; I was starting to wonder how many holdouts like me there were. Which led to this exchange on Twitter

Tuesday, January 24, 2017

Notes on a Conversation with 10X

I've been remiss in writing up a piece on 10X Genomics based on a phone discussion last week with Michael Schnall-Levin (VP Computational Biology and Applications) and Anup Parikh (Director, Product Marketing).  I always appreciate companies reaching out to me and spending time to educate me on their products and plans, and this was a very interesting and enjoyable conversation.