Mihail ZdravkovApr 7
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
nf-coreMar 31

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

Release mag 5.4.2 - Yellow Frog patch · nf-core/mag

Added #1006 - Add citations and references texts in the utils_nfcore_mag_pipeline subworkflow (by @dialvarezs) Changed #1000 - Update GUNC modules and enable the tool in tests (by @dialvarezs) #...

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nf-coreMar 12

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

Mihail ZdravkovFeb 11

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

nf-coreFeb 2

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

Kuba.SawickiDec 7

Our paper “Giant chromosomes of a tiny plant” is out in
@GigaScience
! We present a T2T genome assembly of the simple thalloid liverwort Apopellia endiviifolia with truly giant chromosomes. 🌱🧬 #plantgenomics #T2T #liverworts #nanoporeSequencing
@nanopore

tinyurl.com/m8tkkxd3

nf-coreDec 5

Pipeline release! nf-core/mag v5.3.0 - mag 5.3.0 - Rainbow Rattlesnake!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.3.0

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

nf-coreNov 7

Pipeline release! nf-core/mag v5.2.0 - mag 5.2.0 - Puce Pangolin!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.2.0

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

nf-coreOct 17, 2025

Pipeline release! nf-core/bacass v2.5.0 - nf-core/bacass v2.5.0!

Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.5.0

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

nf-coreSep 30, 2025

Pipeline release! nf-core/mag v5.0.0 - mag 5.0.0 - Green Squirrel!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.0.0

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

Release mag 5.0.0 - Green Squirrel · nf-core/mag

Added #718 - Add support for independent long-read metagenomic assembly (requested by @ljmesi and many others, added by @muabnezor) #718 - Added metaMDBG and (meta)Flye as long read assemblers (ad...

GitHub