#nanopore — Public Fediverse posts

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

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

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/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

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

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

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

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

Adaptive sampling #WGS is moving genomics from lab bench to bedside. In our latest work, we deliver variant, structural & methylation insights on @nanopore's PromethION platform with molecular signals emerging in minutes, not days. Watch this space 👀
#clinicalai #genomicsforhealth #nanopore #multiomics

https://www.medrxiv.org/content/10.1101/2025.10.02.25336569v1

Can you imagine calling #m6A modifications from raw #RNA #nanopore reads just with #basecalling?

Let me introduce you to #m6ABasecaller

https://doi.org/10.1101/2023.11.13.566801

Can you imagine calling #m6A modifications from raw #RNA #nanopore reads just with #basecalling?

Let me introduce you to #m6ABasecaller

https://doi.org/10.1101/2023.11.13.566801

Find out what happens when Merkulov et al. combine #Cas9-targeted #Nanopore sequencing (CANS) with the novel pipeline NanoCasTE to trace both #genetically inherited and #somatic #TEIs in plants!
https://doi.org/10.1111/jipb.13555
@wileyplantsci
#JIPB #PlantSci #Arabidopsis #PlantScience #botany

#Minimap2 #Rust library release: minimap2 v0.1.13+minimap2.2.26

* Latest minimap2 stable release (2.26)
* with_seq function
* hopefully compiles for MacOS / aarch64.
* Still struggling with SSE, I recommend using simde feature
* Soft-clipping properly in CIGAR strings but use caution. Happy to work on it more.

https://github.com/jguhlin/minimap2-rs

https://crates.io/crates/minimap2

And the -sys crate
https://crates.io/crates/minimap2-sys

#bioinformatics #genomics #nanopore #pacbio

#Minimap2 #Rust library release: minimap2 v0.1.13+minimap2.2.26

* Latest minimap2 stable release (2.26)
* with_seq function
* hopefully compiles for MacOS / aarch64.
* Still struggling with SSE, I recommend using simde feature
* Soft-clipping properly in CIGAR strings but use caution. Happy to work on it more.

https://github.com/jguhlin/minimap2-rs

https://crates.io/crates/minimap2

And the -sys crate
https://crates.io/crates/minimap2-sys

#bioinformatics #genomics #nanopore #pacbio

Can someone suggest software/pipelines for analysis of alternative #splicing from long-read #RNAseq (from #Nanopore #MinION)? Basically, I'd like to quantify abundance of different splicing variants in different samples. #bioinformatics

So - with kit v14 and what seems to be pretty great #nanopore read qualities across the board (still itching to test out duplex calls on existing data and compare), should we reconfigure #minimap2 options for longread mapping? Or would using asm5 preset suffice?

Anyone with v14 reads with some insights?

#bioinformatics #sequencing #genomics

Is there any one familiar with analysis of #nanopore #longreads ?

I'm having some bizarre issues when using #minimap2 to align them and I'm almost out of ideas of what to try next...

Here's an explanation of my issue

https://www.biostars.org/p/9546698/

#sequencing #alignment #bioinformatics

Is there any one familiar with analysis of #nanopore #longreads ?

I'm having some bizarre issues when using #minimap2 to align them and I'm almost out of ideas of what to try next...

Here's an explanation of my issue

https://www.biostars.org/p/9546698/

#sequencing #alignment #bioinformatics

A release note for #bioinformatics #basecalling fans! We've released wf-basecalling: wrapping the experimental #nanopore #Dorado caller in an easy to use #nextflow pipeline, and incorporated it into wf-human-variation 0.4.0 for an end-to-end base calls to variant calls workflow!
https://labs.epi2me.io/epi2me-labs-22.11.01-release/

@benjaminv Should've tagged #gpu #resources #nanopore #basecalling as well ;) This looks interesting, going to check it out -- thanks!

And to put it in hashtags, in case that makes it easier to find...
#PARP
#ADPribosylation
#posttranslationalmodification
#PTM
#biochemistry
#cellbiology
#nanopore
#RNA
#proteins
#biophysics
#condensates
#SustainableScience
#greenlabs
#womeninscience
#womeninstem