Mastodawn

NFDI4Microbiota Oct 4, 2024

📢 New workshop announcement: Falk Hildebrand - @earlhaminst and Quadram Institute, UK - will join the #NFDI4Microbiota Annual Conference and give an overview of different #amplicon #sequencing pipelines and their practical applications on December 5th. He will show how to install and run the #LotuS2 pipeline on #Linux and how to process and analyse microbial data in #r

👉 Interested? Register here for free: https://events.hifis.net/event/1756/
#FAIR #OpenScience
@Helmholtz_HZI @ZBMED @NFDI

NFDI4Microbiota Annual Conference -Services for the community (Community Registration)

The 3rd NFDI4Microbiota Annual Conference will take place from December 4th to 5th in the Kubus (UFZ, Leipzig). On two days we are diving deep into the main topics of NFDI4Microbiota: The services we offer for YOUR research cycle How to make YOUR data FAIR and Open There will be Poster Sessions on each day with additional services, such as a software marketplace and Data Steward consultation. The days are starting with interesting keynotes, followed by a comprehensive overview on the...

HIFIS and Helmholtz Events (Indico)

nf-core Aug 5, 2024

Pipeline release! nf-core/ampliseq v2.11.0 - Ampliseq Version 2.11.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.11.0

#16s #18s #amplicon-sequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomic-classification #taxonomic-profiling #nfcore #openscience #nextflow #bioinformatics

Release Ampliseq Version 2.11.0 · nf-core/ampliseq

nf-core/ampliseq version 2.11.0 - 2024-08-06 Summary of changes This update is mostly about reference taxonomy databases: added reference databases sbdi-gtdb=R09-RS220-1 for DADA2 added reference ...

GitHub

nf-core Jun 27, 2024

Pipeline release! nf-core/ampliseq v2.10.0 - Ampliseq Version 2.10.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.10.0

Release Ampliseq Version 2.10.0 · nf-core/ampliseq

nf-core/ampliseq version 2.10.0 - 2024-06-27 Summary of changes added ANCOM-BC for differential abundance analysis updated reference databases for sbdi-gtdb & gtdb with R08-RS214-1 and R09-RS220, ...

GitHub

nf-core Apr 3, 2024

Pipeline release! nf-core/ampliseq v2.9.0 - Ampliseq Version 2.9.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.9.0

Release Ampliseq Version 2.9.0 · nf-core/ampliseq

nf-core/ampliseq version 2.9.0 - 2024-04-03 Summary of changes added multiple regions analysis (including 5R / SMURF / q2-sidle), integrating pipesidle and its software container with 1 & 2. templ...

GitHub

Peter Cock Feb 7, 2024

If this all-singing-all-dancing new PCR machine works as well is it sounds http://omicsomics.blogspot.com/2024/02/iconpcr-super-flexible-qpcr.html (blog post from @OmicsOmics) it would be amazing for a bunch of stuff including #metabarcoding #amplicon sequencings where #eDNA and other samples are often at different concentrations.

iconPCR: Super-Flexible qPCR Thermocycler Oft Dreamed, Now Delivered

Has there ever been a product you’ve just wanted to have, but it doesn’t exist? That keeps popping up in discussions - “if only we had X thi...

Kostas Kormas Feb 21, 2023

Primer on #microbiome analysis (with #amplicon #sequencing of #phylogenetic marker #genes

https://intomed.bio.uth.gr/primer-on-microbiome-analysis/

@jobRxiv @academicchatter @academicsunite
#academicchatter @openscience @phdlife @PhD_Genie @phdstudents
#phdlife #highereducation #postdoclife #research #studyabroad #hostmicrobiota #hostmicrobe #microbialecology #microbeinteractions #symbiosis
@MicrobioJC @IMPACTT @openscience

Primer on microbiome analysis - Intomed

Get information about INTOMED project partners and researchers from 3 Universities, 5 Research Institutes and one company.

Intomed

Jon Moller Jan 27, 2023

The final first author publication of my #PhD in @timreadmicro 's lab is now online at Microbiology Spectrum! Enjoy! #amplicon #nanopore #antibioticresistance #infectiousdiseases #bacteriology https://journals.asm.org/doi/10.1128/spectrum.02728-22

EPPIcenter at UCSF Dec 19, 2022

Exploring SSAfrica plasmodium genetic diversity using microsatellite variants & SNPs in resistance genes

@malariagenomics
@epiverse
#Malaria #genomic #microsatellite #genotyping #amplicon
https://www.nature.com/articles/s41598-022-26625-w

Plasmodium malariae structure and genetic diversity in sub-Saharan Africa determined from microsatellite variants and linked SNPs in orthologues of antimalarial resistance genes - Scientific Reports

Plasmodium malariae, a neglected human malaria parasite, contributes up to 10% of malaria infections in sub-Saharan Africa (sSA). Though P. malariae infection is considered clinically benign, it presents mostly as coinfections with the dominant P. falciparum. Completion of its reference genome has paved the way to further understand its biology and interactions with the human host, including responses to antimalarial interventions. We characterized 75 P. malariae isolates from seven endemic countries in sSA using highly divergent microsatellites. The P. malariae infections were highly diverse and five subpopulations from three ancestries (independent of origin of isolates) were determined. Sequences of 11 orthologous antimalarial resistance genes, identified low frequency single nucleotide polymorphisms (SNPs), strong linkage disequilibrium between loci that may be due to antimalarial drug selection. At least three sub-populations were detectable from a subset of denoised SNP data from mostly the mitochondrial cytochrome b coding region. This evidence of diversity and selection calls for including P. malariae in malaria genomic surveillance towards improved tools and strategies for malaria elimination.

Nature

EPPIcenter at UCSF Nov 23, 2022

Great explainer by
@malariagenomics

Send to relatives prior to Thanksgiving dinner!

https://malariagen.net/news-events/news-article/what-amplicon-sequencing

@malariagenomics
#amplicon #malaria #genomics #bioinformatics #sequencing

Jim Downie Nov 15, 2022

Hi all, curious if anyone has run into this kind of issue before? We're quantifying our #amplicon #PCR reactions for #Metabarcoding using PicoGreen prior to normalisation, but we're sometimes getting high concentrations despite no band being visible on a gel. For ITS it’s only at 61 ng/ul that there’s a 50/50 chance of seeing a band. Any idea what might be going on?

#Microbiology #MolecularBiology #labwork