Soeren Michael Karst

Assistant Professor at Columbia University Fertility Center

[Soeren Michael Karst @SorenKarst]

@ChrisVollmers Hi Chris. Love the R2C2 concept and very interesting combining it with UMIs. I got some questions. Would it be okay if I shoot you a DM?

[Soeren Michael Karst @SorenKarst]

@Garrettroph Found something similar some years ago. https://t.co/23PRgKJq0J . Linked the plasmids by coverage profiles and duplicated regions.

[Soeren Michael Karst @SorenKarst]

@mattloose @nanopore Looking great. What Promethion platform are you using? P2?

[Soeren Michael Karst @SorenKarst]

@weisbergaj @JasonWilliamsNY We and others I talked to have observed a general shift downwards in N50 when moving from LSK109 to LSK114. On top of this I have had issues with short fragments and adapters when using SFE https://t.co/70mn7nMcFo .

[Soeren Michael Karst @SorenKarst]

@kirk3gaard @iiSeymour @nanopore 16S amplicons?

[Soeren Michael Karst @SorenKarst]

@AW_NGS @nanopore @Ferchucky @KeyGeneInfo Looks Great. Any short fragment removal pre library prep?

[Pranav Sampara @pranav_sampara]

If you are interested in modeling microbiomes, do come visit me today at poster 17.434. I will also pitch this poster in Auditorium B at 3:22 PM. Excited to talk about multi-omic approaches to resolve physiological traits of functionally degenerate organisms!
@RyanZiels #ISME18

[Mads Albertsen @MadsAlbertsen85]

Why do we use 2 primers in amplicon studies (rRNA/functional genes)? Now you can use 1... and using @nanopore + UMIs you get perfect long amplicons (5 kbp+). #ISME18 come and chat to @EmilAarre95 Poster 127 today! 1/2

[Mads Albertsen @MadsAlbertsen85]

Want to know the potential and limits of 100 Gbp++ @Nanopore metagenomics for recovering HQ MAGs - without short-read sequencing? Come and discuss with Mantas Sereika at #ISME18 poster 124. Also... 1/2

[Mads Albertsen @MadsAlbertsen85]

How do we supercharge MAG recovery in metagenomics? We think the next frontier is hidden in utilizing the modification signal in @nanopore sequencing! Come and discuss the nitty gritty details with Søren #ISME18 poster 082. also ... 1/2

[Mads Albertsen @MadsAlbertsen85]

Ever wondered how few sequencing reads are needed for microbiome-based diagnostics and how it depends on the choice of classification tool? Or just fancy a trip down the Machine Learning rabbit hole? Come discuss ML, classification, and CRC with Sebastian #ISME18 at poster 435!

[Mads Albertsen @MadsAlbertsen85]

Come by #ISME18 poster 369 and discuss how Morten is using @nanopore to diagnose sepsis in hours instead of days using bacterial cell-free DNA in blood samples.

[Mads Albertsen @MadsAlbertsen85]

How do you generate and analyze 10.000 metagenomes across a country? Come and discuss automatization, library-downscaling, and bioinformatics with Thomas #ISME18 poster 088. + how do we integrate vast metadata from a subset of samples to connect macro and micro-diversity?

[Mads Albertsen @MadsAlbertsen85]

Populating the tree-of-life with a genome pr. species is a moonshot mission that I think is realistic within a decade! Come and tell me why it is bullshit and then let's discuss how to join forces to get it done! #ISME18 poster 170! pst.... we are recruiting at all levels!

[Ryan Ziels @RyanZiels]

Are you interested in modeling microbiomes? Check out our new paper where we combine ‘omics with process modeling to resolve the kinetics of functional groups based on their physiological traits. This is a great milestone in @pranav_sampara’s PhD! https://t.co/DEFhA7Nsqd 1/

[Soeren Michael Karst @SorenKarst]

@miles_benton @mrsquooriosity Great. I really appreciate it. No need to report back I got sufficient leads to guide my troubleshooting.

[Soeren Michael Karst @SorenKarst]

I have encountered a problem with ONT adaptive sampling experiments. Initial loading and run is successful, but after flushing and reloading the same library little to no pores are actively sequencing. Anyone else experienced this? @mattloose @alexomics https://t.co/6sg9ivluHD

[Soeren Michael Karst @SorenKarst]

@miles_benton @mrsquooriosity Thanks Miles. Really helpful. So with 50% ish loss during library prep you would end up with 1.5 ug of library split in 3. So loading around 500ng or 100 fmol if mean length is around 8kbp? Do you extend endprep/ligation time?

[Soeren Michael Karst @SorenKarst]

@miles_benton @mrsquooriosity @mattloose @alexomics Thank you Miles! That looks great. Can you reveal some more details? MinION or GridION. Wash kit version. Library input amount. N50.

[Soeren Michael Karst @SorenKarst]

@mattloose @miles_benton @mrsquooriosity @alexomics Thank you for the feedback. I agree. We tested with and without adaptive sampling after wash/reload and still very few active pores out of many available. The pores that were active were in pore a lot of the time.

[Soeren Michael Karst @SorenKarst]

@nanopore