Deep Seq

Core Next Generation Sequencing facility at the University of Nottingham. Experts in Nanopore, Illumina and Sanger sequencing

[Deep Seq @DeepSeqNotts]

Hey @nanopore we have a weird blocking pattern on our flowcell... can you help?

[Deep Seq @DeepSeqNotts]

Just a few flowcells to return to @nanopore

[Deep Seq @DeepSeqNotts]

We have an opportunity for someone to join our fabulous bioinformatics team - https://t.co/2R4zxqUsjz - you will get to work with @nanopore @illumina @bionanogenomics @10xGenomics and more! Please retweet and dm for info!

[Michael Hubank @generoom]

Rapid #genome-wide copy number profiling using adaptive sampling on @nanopore by @mattloose and the amazing team @DeepSeqNotts
Real potential for clinical application.

[Matt Loose @mattloose]

This gif is from one sample of three run on a single @nanopore promethION flow cell. Frankly I'm super impressed at the performance though there is headroom for more improvements. We ran the same libraries as on gridION and have updated our preprint here. https://t.co/oZwRN8vji0

[Deep Seq @DeepSeqNotts]

Happy Christmas all!

[Deep Seq @DeepSeqNotts]

Hey @nanopore we have a weird blocking pattern on our flowcell... can you help?

[Matt Loose @mattloose]

We've put out a short preprint today showing some updates in Readfish for @nanopore adaptive sampling. https://t.co/GQJJkIql33 @alexomics is giving a talk shortly at the #nanoporeconf about this - but a short thread here.

[Matt Loose @mattloose]

Earlier this week we put out a couple of preprints (https://t.co/tDtMuyAOLF https://t.co/RF3f3Tr5KE) describing minoTour https://t.co/veMHrXt2J2, an @nanopore tool we have been developing for several years. A bit of a 🧵

[Matt Loose @mattloose]

I still remember the first time I saw data from @scalene showing ultra long reads (N50>=100kb) were possible. Since then we and others (especially @DrT1973) have worked to get longer reads. This weekend we tested the @circulomics @nanopore ultra long kits. Wow! 19.49 Gb N50 143kb

[Deep Seq @DeepSeqNotts]

Well @nanopore - always seems to happen this time of year... bit of a bug in readfish but sure we will sort it out soon....

[Deep Seq @DeepSeqNotts]

Well @nanopore - always seems to happen this time of year... bit of a bug in readfish but sure we will sort it out soon....

[Matt Loose @mattloose]

So - our ReadFish paper came out on Monday https://t.co/LWx6m1HHXZ using GPU - but what if you only have a laptop? Here's an update from @alexomics to our tools that enable ReadFish on Mac, Linux or Windows with no additional GPU or compute. https://t.co/CgicPm4nUH for details.

[Deep Seq @DeepSeqNotts]

One for #nanoporeconf

[Matt Loose @mattloose]

So - our ReadFish paper came out on Monday https://t.co/LWx6m1HHXZ using GPU - but what if you only have a laptop? Here's an update from @alexomics to our tools that enable ReadFish on Mac, Linux or Windows with no additional GPU or compute. https://t.co/CgicPm4nUH for details.

[John Tyson @DrT1973]

Many application spin out of this on the fly selective sequencing. Tunable custom target panels to genome gap filling..... things get very interesting from here.

[Matt Loose @mattloose]

Great to see this paper out - loads of hard work from @alexomics and many others to get this completed - adaptive sampling on @nanopore sequencers targeting hundreds of genes to depths in excess of 40x on a single flowcell. https://t.co/LWx6m1HHXZ

[10x Genomics @10xGenomics]

Announcing the Visium Spatial Gene Expression for FFPE Scientific Challenge! Share how you’d use Visium Spatial to unlock the full story of your FFPE tissue samples to win an experiment performed by us. Enter by 12/23. Learn more: https://t.co/wvDmoiSCJd #spatial

[Matt Loose @mattloose]

About to start out 100th @nanopore run for covid samples with the team from @DeepSeqNotts . A sad milestone but amazing work by our local team including many from @TeamNUH and @PostdocPat all in support of the work of @CovidGenomicsUK .

[Deep Seq @DeepSeqNotts]

@kirk3gaard @nanopore We recommend this for samples of “unknown origin”. Let’s say someone wants to run a large batch of samples that they’ve extracted. A check on a Flongle (or minion flowcell with a flush) can quickly reveal sample problems. Good sample in - great data out.

[Gemma Clark @ViroGem]

Massive achievement for @TeamNUH Microbiology lab, one of the first labs in the UK to obtain UKAS accreditation for SARS-CoV-2 PCR. A true testament to the hard work & dedication of the micro team, maintaining <24-hr TAT & high quality, end to end service for our patients.

[COVID-19 Genomics UK (COG-UK) Consortium @CovidGenomicsUK]

🧬 The total number of #COVID19 sequences now released is 16,380.

The sequences and analysis are freely available to view 👉 https://t.co/oHHFuIAnGt

[Deep Seq @DeepSeqNotts]

Fantastic to be a part of this innovative distributed network.