#nanopore

Question for #nanopore folks. I'm comparing collaborator's BAM vs mine, generated from same pod5. It looks like the collaborator's BAM has an extra qs: tag missing in mine.

Why would there be a difference? One would think default pod5 commands would record same tags for all output BAM?

#bioinformatics

Pipeline release! nf-core/mag v3.4.0 - mag 3.4.0 - Green Gecko!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/3.4.0

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

Super cool paper (part of PhD thesis): I thought assembling the genome from raw signal isn't practical, but it seems not possible, but yielding results comparable/better to usual approaches: basecalling followed by de novo genome assembly!
#nanopore #GenomeAssembly
https://arxiv.org/pdf/2410.17801
https://arxiv.org/html/2503.02997v1#Ch7

Looking at a funny discrepancy between Dorado 0.8.3 methylation-SUP basecalled bam vs 0.9.1 methylation-SUP basecalled bam.

They're the same raw files with same models, only Dorado version are different.

Left, 0.8.3, right, 0.9.1

That looks like one heck of a discrepancy for a few version numbers on basecalling software.

#bioinformatics #nanopore

What do #nanopore #sequencing #bioinformatics folks think about this one? New preprint on hashing raw nanopore signals and using them directly for de-novo assembly.

https://arxiv.org/abs/2503.02997v1

Hypothetical blow5-to-assembly pipe would be interesting, though figuring it out is way out of my depth.

Pipeline release! nf-core/scnanoseq v1.1.0 - nf-core/scnanoseq v1.1.0 - Iron Alligator!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.1.0

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

shamelessly sharing our recent work: Rapid and accurate #demultiplexing of
direct #RNA #nanopore sequencing datasets with SeqTagger
#paper
https://genome.cshlp.org/content/early/2025/01/29/gr.279290.124.full.pdf

Pipeline release! nf-core/taxprofiler v1.2.3 - v1.2.3 - Bouncy Basenji Patch!

Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.3

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

#nanopore #OxfordNanopore #NanoporeSequencing so just noticed that the 48 pack flowcells is no longer available from the Nanopore store. That is a big price hike for sequencing facilities who usually orders a big pack at a time. @nanopore

Shamelessly sharing our latest publication: De novo basecalling of #RNA #modifications at single molecule and nucleotide resolution
#nanopore
https://link.springer.com/epdf/10.1186/s13059-025-03498-6?sharing_token=IytKQ2p-kKbfSMJeCUsTt2_BpE1tBhCbnbw3BuzI2ROlz0B3e9LQUoHA9qh6NODgonYuX1G1GMfsxEe_sTuS_e_GRybSYX9mxrEoeASxC5RIlpmlV0mD6YesQ7BOjIbYdaxcUKYz3q8l2T2_bvSlO8Tykxj3ICWTyjPsKAmQ36s%3D

Great blog post about new Roche's #Sequencing By Expansion (SBX).
Pre-print is also released already.
#nanopore
https://omicsomics.blogspot.com/2025/02/roche-xpounds-on-new-sequencing.html
https://doi.org/10.1101/2025.02.19.639056

Pipeline release! nf-core/mag v3.3.1 - mag 3.3.1 - [2025-03-13]!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/3.3.1

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

Use of massive DNA barcoding to monitor biodiversity: a test on
forest soil fauna

https://www.biorxiv.org/content/10.1101/2025.02.07.636998v1

#megabarcoding #soil #DNAbarcoding #nanopore #biodiversity

"Here we report on voltage-gated solid-state nanopores by electrically tunable chemical reactions. We demonstrate repetitive precipitation and dissolution of metal phosphates in a pore through manipulations of cation flow by transmembrane voltage. Under negative voltages, precipitates grow to reduce ionic current by occluding the nanopore, while inverting the voltage polarity dissolves the phosphate compounds reopening the pore to ionic flux."

https://www.nature.com/articles/s41467-025-56052-0

#nanopore #biosensor

Pipeline release! nf-core/taxprofiler v1.2.2 - v1.2.2 - Bouncy Basenji Patch!

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

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

Pipeline release! nf-core/mag v3.3.0 - mag 3.3.0 - Red Reindeer!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/3.3.0

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

Apparently, I am Mr. August for a patent of a protocol for #nanopore simultaneous sequencing of long and short RNAs
https://www.biorxiv.org/content/10.1101/2022.12.16.520507v1.full
#UNM

Today was a special day. #nanopore #LongReadSequencing

Very excited to dig into the paper - tool & methodology the authors developed could save lots of headaches for my current sequencing project.

Can anyone reach the linked GitHub URL on the published article though? Entire NanoConsensus repo seems to 404 on my end.
#bioinformatics #nanopore #sequencing

Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites | Nature Communications
https://www.nature.com/articles/s41467-024-54368-x

Pipeline release! nf-core/taxprofiler v1.2.1 - v1.2.1 - Bouncy Basenji Patch [2024-11-28]!

Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.1

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