#nanopore — Public Fediverse posts

Single-molecule #m6A profiling reveals position-dependent #mRNA regulation and non-canonical roles for Ythdf2 in early embryogenesis
#zebrafish #nanopore #paper
https://www.biorxiv.org/content/10.64898/2026.07.03.736379v1

Single-molecule #m6A profiling reveals position-dependent #mRNA regulation and non-canonical roles for Ythdf2 in early embryogenesis
#zebrafish #nanopore #paper
https://www.biorxiv.org/content/10.64898/2026.07.03.736379v1

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.1 - v2.0.1 - Crazy Corgi Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.1

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.1 - v2.0.1 - Crazy Corgi Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.1

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.1 - v2.0.1 - Crazy Corgi Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.1

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.1 - v2.0.1 - Crazy Corgi Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.1

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.1 - v2.0.1 - Crazy Corgi Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.1

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

What I'm also doing is assessing 3rd party sequencing vendor ONT output quality using some variations of these tools. Feel free to get in touch if you have a sequencing vendor you want to either recommend or have assessed!

#sequencing #microbiology #archaea #ONT #nanopore #bioinformatics

What I'm also doing is assessing 3rd party sequencing vendor ONT output quality using some variations of these tools. Feel free to get in touch if you have a sequencing vendor you want to either recommend or have assessed!

#sequencing #microbiology #archaea #ONT #nanopore #bioinformatics

I've been working on a small Julia library for working with raw nanopore sequencing signals.

It's still under development and not very mature, but maybe someone may find it useful and want to experiment with it. It provides functionality for signal-to-sequence alignments, basic signal scaling and segmentation, poly(A) tail detection, etc. If you stumble at issues or have ideas for new functionality or feedback, please reach out.

https://mzdravkov.com/docs/NanoporeSignals.jl/

#julialang #nanopore #bioinformatics

I've been working on a small Julia library for working with raw nanopore sequencing signals.

It's still under development and not very mature, but maybe someone may find it useful and want to experiment with it. It provides functionality for signal-to-sequence alignments, basic signal scaling and segmentation, poly(A) tail detection, etc. If you stumble at issues or have ideas for new functionality or feedback, please reach out.

https://mzdravkov.com/docs/NanoporeSignals.jl/

#julialang #nanopore #bioinformatics

Pipeline release! nf-core/bacass v2.6.0 - nf-core/bacass v2.6.0 - Crimson Titanium Seahorse!
Simple bacterial assembly and annotation pipeline
Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.6.0

#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/bacass v2.6.0 - nf-core/bacass v2.6.0 - Crimson Titanium Seahorse!
Simple bacterial assembly and annotation pipeline
Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.6.0

#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Performance test of QNome nanopore sequencer. Looks very interesting - I'm always on the lookout for alternate platforms for Binomica. More reason for us to build platform agnostic squiggle/QC tools for the future!

https://www.biorxiv.org/content/10.64898/2026.04.29.721586v1

#bioinformatics #ONT #nanopore #microbiology

Performance test of QNome nanopore sequencer. Looks very interesting - I'm always on the lookout for alternate platforms for Binomica. More reason for us to build platform agnostic squiggle/QC tools for the future!

https://www.biorxiv.org/content/10.64898/2026.04.29.721586v1

#bioinformatics #ONT #nanopore #microbiology

I went through a bunch of PCIe usb cards that can allow the P2 Solo to communicate with MinKnow (per ONT connecting those devices to a PCIe/USB is a No-No). Can verify we have liftoff w the Startech 20gbps , but not the U3142c. May need to ⬆️ Linux buffer size for DAQ #nanopore

I went through a bunch of PCIe usb cards that can allow the P2 Solo to communicate with MinKnow (per ONT connecting those devices to a PCIe/USB is a No-No). Can verify we have liftoff w the Startech 20gbps , but not the U3142c. May need to ⬆️ Linux buffer size for DAQ #nanopore

I went through a bunch of PCIe usb cards that can allow the P2 Solo to communicate with MinKnow (per ONT connecting those devices to a PCIe/USB is a No-No). Can verify we have liftoff w the Startech 20gbps , but not the U3142c. May need to ⬆️ Linux buffer size for DAQ #nanopore

Pipeline release! nf-core/taxprofiler v2.0.0 - v2.0.0 - Crazy Corgi!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.0

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.0 - v2.0.0 - Crazy Corgi!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.0

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.0 - v2.0.0 - Crazy Corgi!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.0

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.0 - v2.0.0 - Crazy Corgi!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.0

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v2.0.0 - v2.0.0 - Crazy Corgi!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/2.0.0

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Dear Nanopore folks, could you give an advice about an issue that my lab has with direct RNA sequencing on MinION. We're doing RNA004 sequencing of various samples and again and again, there's a staggering amount of reads with just repetitive AAG triplet. This happens for weird IVT RNA and perfectly normal yeast or HEK cells. I'm using Dorado 1.4.0 with the 5.3.0 sup model. Looks to me like the open channel or some kind of stalling is just called as this kmer.
#nanopore #nanoporesequencing

Dear Nanopore folks, could you give an advice about an issue that my lab has with direct RNA sequencing on MinION. We're doing RNA004 sequencing of various samples and again and again, there's a staggering amount of reads with just repetitive AAG triplet. This happens for weird IVT RNA and perfectly normal yeast or HEK cells. I'm using Dorado 1.4.0 with the 5.3.0 sup model. Looks to me like the open channel or some kind of stalling is just called as this kmer.
#nanopore #nanoporesequencing

https://www.europesays.com/be/10171/ DNA and RNA Analysis Instruments Market in Belgium | Report – IndexBox #Belgium #BiopharmaMarketReport #CapillaryElectrophoresis #DigitalDropletPartitioning(dPCR) #DNAAndRNAAnalysisInstruments #forecast #GeneExpressionAnalysis #GenomicSequencing #Genotyping&MutationDetection #IonTorrent #MarketAnalysis #Nanopore) #NextGenerationSequencing(Illumina #PathogenDetection&Surveillance #RealTimeFluorescenceDetection(qPCR)

https://www.europesays.com/britain/4825/ DNA and RNA Analysis Instruments Market in the United Kingdom | Report – IndexBox #BiopharmaMarketReport #CapillaryElectrophoresis #DigitalDropletPartitioning(dPCR) #DNAAndRNAAnalysisInstruments #forecast #GeneExpressionAnalysis #GenomicSequencing #Genotyping&MutationDetection #IonTorrent #MarketAnalysis #Nanopore) #NextGenerationSequencing(Illumina #PathogenDetection&Surveillance #RealTimeFluorescenceDetection(qPCR) #UK #UnitedKingdom

Pipeline release! nf-core/mag v5.4.2 - mag 5.4.2 - Yellow Frog patch!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.2

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mag v5.4.2 - mag 5.4.2 - Yellow Frog patch!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.2

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Hi everyone 🖖

If you are thinkging about using #nanopore for genomic surveillance in #hospitals, but don't have the #bioinformatics nor command-line skills, don't let that put you off.

'Modernising Medical Microbiology', at @NDMOxford in #Oxford, has developed `OxBreaker': a graphical tool that can help identify budding #outbreaks by #healthcare professionals without having to upload your data to external servers and compromise patient privacy. Worth a read 👇

https://www.biorxiv.org/content/10.64898/2026.03.18.709804

Hi everyone 🖖

If you are thinkging about using #nanopore for genomic surveillance in #hospitals, but don't have the #bioinformatics nor command-line skills, don't let that put you off.

'Modernising Medical Microbiology', at @NDMOxford in #Oxford, has developed `OxBreaker': a graphical tool that can help identify budding #outbreaks by #healthcare professionals without having to upload your data to external servers and compromise patient privacy. Worth a read 👇

https://www.biorxiv.org/content/10.64898/2026.03.18.709804

Pipeline release! nf-core/mag v5.4.1 - mag 5.4.1 - Yellow Frog patch!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.1

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mag v5.4.1 - mag 5.4.1 - Yellow Frog patch!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.1

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

We are delighted to welcome Hannah to our group. She will conduct long-read sequencing to explore plant genomes. We are excited to have her on board and look forward to amazing discoveries ahead!

https://www.izmb.uni-bonn.de/en/pbb/team

#PlantGenomics #LongReadSequencing #Bioinformatics #Nanopore #PlantScience #TeamScience
@boas_pucker

We are delighted to welcome Hannah to our group. She will conduct long-read sequencing to explore plant genomes. We are excited to have her on board and look forward to amazing discoveries ahead!

https://www.izmb.uni-bonn.de/en/pbb/team

#PlantGenomics #LongReadSequencing #Bioinformatics #Nanopore #PlantScience #TeamScience
@boas_pucker

Pipeline release! nf-core/taxprofiler v1.2.6 - v1.2.6 - Bouncy Basenji Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.6

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v1.2.6 - v1.2.6 - Bouncy Basenji Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.6

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/taxprofiler v1.2.6 - v1.2.6 - Bouncy Basenji Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.6

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Does anyone know if an NVidia RTX 4060 can handle an Mk1D MinION with runtime basecalling? ONT's documentation says that the minimum requirement is an RTX 5060, but this sounds a bit crazy. And the difference between the two GPUs is not that big I think.

Also, this will mostly be for dRNA-seq, where we basecall after the run, so would it be okay to run two MinIONs in parallel (without basecalling)?

#nanopore #nanoporeSequencing #OxfordNanopore

Does anyone know if an NVidia RTX 4060 can handle an Mk1D MinION with runtime basecalling? ONT's documentation says that the minimum requirement is an RTX 5060, but this sounds a bit crazy. And the difference between the two GPUs is not that big I think.

Also, this will mostly be for dRNA-seq, where we basecall after the run, so would it be okay to run two MinIONs in parallel (without basecalling)?

#nanopore #nanoporeSequencing #OxfordNanopore

Pipeline release! nf-core/mag v5.4.0 - mag 5.4.0 - Yellow Frog!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.0

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mag v5.4.0 - mag 5.4.0 - Yellow Frog!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.0

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Our latest research article is a proof of concept protocol for combining #Nanopore sequencing with the #Twist Comprehensive Viral Research Panel. A great tool allowing us to study the #virome of clinical patient samples with a targeted #metagenomics approach.
#Research
#Science
#Biology
#Microbiology
#ClinicalDiagnostics

https://www.sciencedirect.com/science/article/pii/S0042682226000048

Our latest research article is a proof of concept protocol for combining #Nanopore sequencing with the #Twist Comprehensive Viral Research Panel. A great tool allowing us to study the #virome of clinical patient samples with a targeted #metagenomics approach.
#Research
#Science
#Biology
#Microbiology
#ClinicalDiagnostics

https://www.sciencedirect.com/science/article/pii/S0042682226000048

new citation:

Design Strategies toward Precise Protein Sequencing with Biological Nanopores (REVIEW)

https://doi.org/10.1021/acs.analchem.5c05662

#science #nanopore #biosensor #bioengineering #engineering #biology #chemistry #biochemistry #sensing #data #datascience #nanotechnology #nanobiotechnology #research #reviewArticle #primaryLiterature

new citation:

Design Strategies toward Precise Protein Sequencing with Biological Nanopores (REVIEW)

https://doi.org/10.1021/acs.analchem.5c05662

#science #nanopore #biosensor #bioengineering #engineering #biology #chemistry #biochemistry #sensing #data #datascience #nanotechnology #nanobiotechnology #research #reviewArticle #primaryLiterature