@SAGRudd

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

 North Norfolk, UK
Joined July 2010
  • Tweets11.8K
  • Following1.2K
  • Followers2.6K
204Media
Stephen Rudd retweeted
Javier Santoyo@jsantoyo20 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…

SeqManager: a web-based tool for efficient sequencing data storage management and duplicate...

AbstractMotivation. Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storag

academic.oup.com
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Stephen Rudd retweeted
antisense.@razoralign3 Dec 2024
Pod5Viewer: a GUI for inspecting raw nanopore sequencing data academic.oup.com/bioinformat…
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Stephen Rudd retweeted
antisense.@razoralign23 Oct 2024
GCI: A continuity inspector for complete genome assembly academic.oup.com/bioinformat…
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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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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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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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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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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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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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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

A guide to reviewing BAM files

In the world of sequencing data analysis, automation reigns supreme. Standardised workflows, such…

epi2me.nanoporetech.com
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“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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EPI2ME hackathon - @IQCB_Mainz @nanopore - Andrea deep diving into @nextflowio parallelisation and parameterisation; it can always be faster
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What you're missing matters! Prost! #Bielefeld #wymm @nanopore – at Munich, Germany
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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!
Oxford Nanopore
@nanopore15 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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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

Querying a VCF file

Anyone working with genomic data from next or third generation sequencing studies is bound to work…

epi2me.nanoporetech.com
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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

EPI2ME 24.02-01 Release

Dear Nanopore Community, We are delighted to release a magnificent collection of updates and…

epi2me.nanoporetech.com
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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!

Input directory structure for EPI2ME workflows

The EPI2ME team strives to make bioinformatics analysis as easy to use and intuitive as possible…

epi2me.nanoporetech.com
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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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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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