Lmst

🚀 Master Statistical Methods for Metatranscriptomics
🗓️ 27–29 Apr | Online

Hands-on R/Bioconductor workshop on data normalization, differential expression, networks & multi-omics integration.

https://www.physalia-courses.org/courses-workshops/metatranscriptomics/

#Metatranscriptomics #Bioinformatics #RStats #Omics

🎉 Huge shout out to everyone who instructed and participated in yesterday's online Meta-*omics #Nextflow Pipeline Community Exhibition Day!

🧑‍🏫 Over 9 hours, we had 15 different pipelines demo'd by their lead developers, and giving an international cohort of participants hands-on experience on running diverse pipelines spanning #metataxonomics, #metagenomics, #metatranscriptomics, and #metaproteomics, as well as a crash-course on the different ways to configure Nextflow pipelines.

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Meta-*omics Nextflow pipeline community exhibition day

Organised by James Fellows Yates

Supported by NFDI4Microbiota, Nextflow Ambassador program, and deNBI

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial of #metagenomics #metataxonomics #metaproteomics #metatranscriptomics pipelines directly from the developers!

Since the first advert: we also have an additional pipeline that will be exhibited (metagenomics-toolkit)

We are almost oversubscribed, so register ASAP, deadline to register is Oct 24th: https://tally.so/r/31qJyQ

Poster advertising an event

Meta-*omics
Nextflow Pipeline
Community Exhibition Day
Do you work with . Want to find out how to
metagenomics, metaxaxonomics, make your analysis more
metaproteomics, metatranscriptomics efficient, scalable, and
datasets? reproducible?
Meet developers for an introduction and practical hands-on demonstration of their meta-*omics Nextflow pipelines!
When is it happening?
December 10th 2025. Times pending
Where is happening?
Online! Platform pending

What do you need?
- Ability to navigate the UNIX command line Online
- Be already familiar with basic theory/concepts pjatform pending of the analysis of your meta-*omics data
- A computer, and an internet connection

Interested? Register your interest and choose your pipeline(s)
https://tally.so/r/31gJyQ

Supported by NFDI4MIcrobiota and NextflowAmbassadors

Poster advertising event

Featured pipelines

nf-core/createtaxdb (nf-co.re/createtaxdb)
nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input FASTA reference genome set in a highly automated and parallelised manner.

Biobakery-nextflow (github.com/BonhamLab/biobakery-nextflow)
Shotgun metagenomics community profiling (taxonomic and functional) of Illumina short read data using the Biobakery suite of tools and databases.

epi2me-labs/wf-metagenomics (github.com/epi2me-labs/wf-metagenomics)
Taxonomic classification of Nanopore sequenced metagenomic sequencing data and identification of antimicrobial resistance (AMR) or virulence genes. It includes an optional step to remove host sequences. It can also be run through the EPI2ME Desktop Application.

nf-core/taxprofiler (nf-co.re/taxprofiler)
nf-core/taxprofiler is a pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It performs in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, with standardised output profiles.

(and more! Please contact James Fellows Yates for the rest of the list - hitting Alt text limits now)

Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial directly from the developers!

Interested? Please register your interest with this link: https://tally.so/r/31qJyQ !

📣 Last call 📣

👨🏾‍💻 Do you develop a #Nextflow #pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics

🎉 Represent your pipeline at an upcoming community 'meta-omics' exhibition day by giving a tutorial!

✏️ Register your interest to demo your pipeline: https://tally.so/r/3Xp7vY

❓ Do you develop a #Nextflow pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics, etc?

🧑‍💻 I'm looking for #bioinformatics developers to give demos of their #opensource pipelines to the scientific community in a ‘Meta-*omics Nextflow pipeline community exhibition day’!

🧑‍🏫 This involves a short presentation and a hands-on tutorial for attendees (we will provide compute resources!)

👋 If this sounds interesting to you, please let me know: https://tally.so/r/3Xp7vY

Do you develop a #Nextflow pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics, etc?

I'm looking for #bioinformatics developers interested in giving demos of their #opensource pipelines to the scientific community in a ‘Meta-*omics Nextflow pipeline community exhibition day’!

This would involve a short presentation and a hands-on tutorial for attendees (we will provide compute resources!)

If this sounds interesting, please let me know: https://tally.so/r/3Xp7vY

Flyer for 'looking for pipeline developers for a Meta-*omics Nextflow pipeline day'. Gives short background on the idea, why developers should participate in demoing their pipeline, and that it will happen online and likely around early December.

Pipeline release! nf-core/metatdenovo v1.3.0 - Release v. 1.3.0!

Please see the changelog: https://github.com/nf-core/metatdenovo/releases/tag/1.3.0

#eukaryotes #metagenomics #metatranscriptomics #prokaryotes #viruses #nfcore #openscience #nextflow #bioinformatics

The whole study is done painstakingly on manual genome annotation and analysis combined with #metatranscriptomics. I wonder, whether metabolic modeling would have predicted the same.

Pipeline release! nf-core/metatdenovo v1.2.0 - nf-core/metatdenovo 1.2.0!

Please see the changelog: https://github.com/nf-core/metatdenovo/releases/tag/1.2.0

#eukaryotes #metagenomics #metatranscriptomics #prokaryotes #viruses #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/metatdenovo v1.1.1 - nf-core/metatdenovo 1.1.1!

Please see the changelog: https://github.com/nf-core/metatdenovo/releases/tag/1.1.1

#eukaryotes #metagenomics #metatranscriptomics #prokaryotes #viruses #nfcore #openscience #nextflow #bioinformatics

Viroid-like “obelisk” agents are widespread in the ocean and exceed the abundance of RNA viruses in the prokaryotic fraction.
#Viroids #Obelisks #HammerheadRibozyme #Metatranscriptomics #UncorrectedManuscript
https://academic.oup.com/ismej/advance-article/doi/10.1093/ismejo/wraf033/8042533

Pipeline release! nf-core/metatdenovo v1.1.0 - Nf-core/metatdenovo 1.1.0!

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

#eukaryotes #metagenomics #metatranscriptomics #prokaryotes #viruses #nfcore #openscience #nextflow #bioinformatics

🦠 Interested in #nextflow & anything 'meta-' ?(#metagenomics, #metabarcoding, #metatranscriptomics, #metaproteomics, #microbes #MicrobialEcology & more!)

📆 Join us next Tuesday 13:00 CEST (3rd September) for an nf-core #bytesize for the #metaomics #nfcore special interest group! (Also on YouTube after!)

🤝 We will introduce how we want the community to work together with #users and #bioinformatics developers to make the best pipelines for anything 'meta-'

ℹ️ Zoom: https://nf-co.re/events/2024/bytesize_sig_meta_omics

Scientists map #soil #RNA to #fungal #genomes to understand #forest ecosystems.

#microbiome #Metatranscriptomics

https://phys.org/news/2024-04-scientists-soil-rna-fungal-genomes.html

Time-resolved analysis of microbial mats - using metatranscriptomics!

Amanda Shelton from Carnegie at #JGI2023

#jgi @LBNLBioSci #microbiology #metagenomics #metatranscriptomics

"**MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities"**

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01562-6

#RNAseq #metatranscriptomics #microbes #bioinformatics #pipeline

Today is the LAST DAY to apply for our joint CBW-IMPACTT Microbiome Analysis Workshop at the early-bird rate! July 5-7, 2023 at the University of Calgary. Apply here: https://bioinformatics.ca/workshops-all/2023-cbw-impactt-microbiome-analysis/

#bioinformatics #workshop #16S #18S #sequencing #shotgunsequencing #metagenomics #genomics #transcriptomics #metatranscriptomics #longread #markergene #functionalannotation #tutorial #statistics #biostatistics #microbiome #microbiota #microbialecology #diversity #betadiversity #differentialabundance

Flyer for the CBW-IMPACTT Microbiome Analysis Workshop. July 5-7, 2023 at the University of Calgary, Alberta, Canada.

Do you want to learn #Metagenomics #Metatranscriptomics #Bioinformatics and #MultiOmics?

Join us in June for this amazing course with Physalia Courses!

https://physalia-courses.org/courses-workshops/course33/

There are still a few seats available!

Thank you to everyone who attended (and taught at) our Bioinformatics Workshop earlier this week at McGill University! Learn more and sign up for updates about future workshops here: https://www.impactt-microbiome.ca/bioinformatics-workshop/

#bioinformatics #workshop #QIIME2 #metagenomics #metatranscriptomics #transcriptomics #functional #analysis #statistics #microbiome #data #datascience

#Metatranscriptomics

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