Genomics and bioinformatics. Impatiently looking for nirvana but discovering the world. Product, projects, and workflows
Joined July 2010
- Tweets 11,807
- Following 1,215
- Followers 2,613
- Likes 1,171
204 Photos and videos
Stephen Rudd retweeted
20 Nov 2025
SeqManager: A Web-Based Tool for Efficient Sequencing Data Storage Management and Duplicate Detection. #SequencingData #DataStorage #DuplicateDetection #Genomics #Bioinformatics @BioinfoAdv
academic.oup.com/bioinformat…
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Stephen Rudd retweeted
3 Dec 2024
Pod5Viewer: a GUI for inspecting raw nanopore sequencing data academic.oup.com/bioinformat…
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Stephen Rudd retweeted
23 Oct 2024
GCI: A continuity inspector for complete genome assembly academic.oup.com/bioinformat…
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Stephen Rudd retweeted
11 Oct 2024
ClairS and ClairS-TO get a big performance bump. Check out the new versions and a technical note 🔗github.com/HKU-BAL/ClairS/bl… to see how we have improved the performance of ClairS and ClairS-TO with new real cancer cell-line datasets and PoN. 1/
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Stephen Rudd retweeted
16 Sep 2024
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
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Stephen Rudd retweeted
16 Sep 2024
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 🤘🚀
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Stephen Rudd retweeted
21 Mar 2024
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.
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Stephen Rudd retweeted
6 Mar 2024
A new dataset. Tumour/Normal pair on kit 14 5khz. Raw data and analysis available from our s3 bucket!
labs.epi2me.io/colo-2024.03/
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Stephen Rudd retweeted
6 Mar 2024
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…
labs.epi2me.io/epi2me-24.03-…
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Stephen Rudd retweeted
5 Mar 2024
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:
labs.epi2me.io/reviewing-bam
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4 Mar 2024
“Do you really need real-time?” - Natalia showing how ‘watchPath’ opens new horizons for at runtime data review #EPI2ME @IQCB_Mainz @nanopore @nextflowio
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4 Mar 2024
EPI2ME hackathon - @IQCB_Mainz @nanopore - Andrea deep diving into @nextflowio parallelisation and parameterisation; it can always be faster
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Stephen Rudd retweeted
27 Feb 2024
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Stephen Rudd retweeted
15 Feb 2024
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!
15 Feb 2024
Our advanced workshop for bioinformaticians offers hands-on experience in developing workflows for nanopore sequence analysis. Bring your laptop and skills and we will provide the coaching and challenges.
Learn more: bit.ly/3HPYrQy #nanoporeconf #wymm
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Stephen Rudd retweeted
12 Feb 2024
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:
labs.epi2me.io/querying-vcf-…
@nanopore #EPI2ME
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Stephen Rudd retweeted
8 Feb 2024
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!
labs.epi2me.io/epi2me-24.02-…
#AGBT #AGBT24
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Stephen Rudd retweeted
22 Jan 2024
We get lots of questions on how input data should look for analysis with @nanopore EPI2ME workflows, Julian has put together a nice explanation!
labs.epi2me.io/input-data/
If you have any requests for blog posts we'd be happy to hear your ideas!
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Stephen Rudd retweeted
22 Jan 2024
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
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Stephen Rudd retweeted
19 Jan 2024
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:
labs.epi2me.io/bed-bugs/
background:
labs.epi2me.io/beg-bugs-intr…
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