Stephen Rudd

Genomics and bioinformatics. Impatiently looking for nirvana but discovering the world. Product, projects, and workflows

[Javier Santoyo @jsantoyo]

SeqManager: A Web-Based Tool for Efficient Sequencing Data Storage Management and Duplicate Detection. #SequencingData #DataStorage #DuplicateDetection #Genomics #Bioinformatics @BioinfoAdv
https://t.co/l23n4dy2q5

[antisense. @razoralign]

Pod5Viewer: a GUI for inspecting raw nanopore sequencing data https://t.co/524o7I0s9t

[antisense. @razoralign]

GCI: A continuity inspector for complete genome assembly https://t.co/r4EgfQldL1

[Ruibang Laurent Luo @aquaskyline]

ClairS and ClairS-TO get a big performance bump. Check out the new versions and a technical note 🔗https://t.co/1cQea6jTD3 to see how we have improved the performance of ClairS and ClairS-TO with new real cancer cell-line datasets and PoN. 1/

[Oxford Nanopore @nanopore]

We continue to commit to a unified EPI2ME experience.

We've launched the #EPI2ME cloud enabling EPI2ME in the cloud or locally - data analysis for all.
#nanoporeconf

[Rachel Rubinstein @rgrubinstein]

live from #NCMBOS2024 EPI2ME Cloud is finally released for everyone! we can’t wait to see what incredible bioinformatics analysis you all will do on the platform 🤘🚀

[Nic Houghton @40PercentGerman]

Learning German isn't about studying grammar or memorising Der, Die, Das.

No, it's knowing 3 things:

- when to interject with a solid "Wirklich!"

- when to deliver a devastating "Doch!"

- the optimum exasperated pitch for shouting "HALLO!" while in a supermarket queue.

[Matthew Parker @bioinfomatt]

A new dataset. Tumour/Normal pair on kit 14 5khz. Raw data and analysis available from our s3 bucket!

https://t.co/Ma9kT13R92

[Matthew Parker @bioinfomatt]

Lots of new workflow features and updates in this months @nanopore #EPI2ME release. Highlights include Salmonella Serotyping in wf-bacterial-genomes for all your food safety needs, and a new CNV caller in wf-human-variation (Spectre @sedlazeck) and…

https://t.co/cecmqzUpmc

[Matthew Parker @bioinfomatt]

A key skill in bioinfo is assessment of raw seq data. Tools like IGV are useful to view aligned reads & variants. I've manually reviewed 1000s of variants and it's worth knowing what a real variant looks like! From Sirisha in the @nanopore #EPI2ME team:

https://t.co/Ho9bmEZKZ7

[Stephen Rudd @SAGRudd]

“Do you really need real-time?” - Natalia showing how ‘watchPath’ opens new horizons for at runtime data review #EPI2ME @IQCB_Mainz @nanopore @nextflowio

[Stephen Rudd @SAGRudd]

EPI2ME hackathon - @IQCB_Mainz @nanopore - Andrea deep diving into @nextflowio parallelisation and parameterisation; it can always be faster

[Tobias Busche @BuscheTobias]

What you're missing matters! Prost!
#Bielefeld #wymm @nanopore

[Matthew Parker @bioinfomatt]

The @nanopore EPI2ME team will be helping deliver this workshop. Come learn how we develop our workflows so you can deploy your own in EPI2ME!

[Matthew Parker @bioinfomatt]

VCF files can be annoying to query if you don't know how. Andrea, who is developing our large human workflows which often produce unwieldy VCF files has written a blog post on how to do it:

https://t.co/OMJLIjiyVB

@nanopore #EPI2ME

[Matthew Parker @bioinfomatt]

Absolutely mega release from the @nanopore EPI2ME team including big speed ups for wf-human-variation, a new BAC mode for wf-clone- validation, tumour only more for wf-somatic-variation and many many more improvements and bug fixes!

https://t.co/OIeCbY3J3c

#AGBT #AGBT24

[Matthew Parker @bioinfomatt]

We get lots of questions on how input data should look for analysis with @nanopore EPI2ME workflows, Julian has put together a nice explanation!

https://t.co/Zk4shFoZud

If you have any requests for blog posts we'd be happy to hear your ideas!

[Oxford Nanopore @nanopore]

We're making bioinformatics more accessible.

With #EPI2ME anyone can now run any @nextflowio workflow — without any bioinformatics experience.

Have a new workflow? Simply import it & share with your non-bioinformatician colleagues to use from the point & click interface. 1/2

[Matthew Parker @bioinfomatt]

You might have thought bed bugs was a very 2023 phenomenon.... wrong. Check out the new @nanopore tool "bed bugs" for the validation and generation of useful statistics from your bed files for adaptive sampling!

tool:
https://t.co/POo9KiXo0R

background:
https://t.co/MBwYv6mNt3