Pipeline release! nf-core/ampliseq v2.14.0 - Ampliseq Version 2.14.0!
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.14.0
#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/ampliseq v2.13.0 - Ampliseq Version 2.13.0!
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.13.0
#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics
đź“° Happy to announce the publication in @PeerCommunityJournal of our analysis of #VaginalMicrobiota dynamics.
🦠This work provides unprecedented insights into the occurrence of #dysbioses.
Thanks to the #women participating in the #PAPCLEAR study at CHU Montpellier (France) 🙏
The model (all in #RStan) was built by @tsukushi_kamiya and the #16S sequencing of over 2.000 samples was done in Jacques Ravel's lab. This work stems from the @ERC_Research #EVOLPROOF project.
https://peercommunityjournal.org/articles/10.24072/pcjournal.527/
Heureux d'annoncer la publication dans @PeerCommunityJournal de notre analyse de la dynamique du #MicrobioteVaginal.
Ces travaux sont issus de l'étude #PAPCLEAR promue par le #CHU_Montpellier et financée par l' @ERC_Research, qui représente l'un des suivis les plus longs à ce jour.
Le magnifique modèle statistique (tout en #RStan) a été réalisé par @tsukushi_kamiya et le séquençage #16S de plus de 2000 échantillons réalisé dans le laboratoire de Jacques Ravel.
https://peercommunityjournal.org/articles/10.24072/pcjournal.527/
Pipeline release! nf-core/ampliseq v2.12.0 - Ampliseq Version 2.12.0!
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.12.0
#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics
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
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
#16s #18s #amplicon-sequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomic-classification #taxonomic-profiling #nfcore #openscience #nextflow #bioinformatics
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
#16s #18s #amplicon-sequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomic-classification #taxonomic-profiling #nfcore #openscience #nextflow #bioinformatics
Tropical Cyclone #16S has developed in the South Indian Ocean.
See the latest forecast here: https://zoom.earth/storms/16s-2024/
Happy to have contributed, w Thorsten Stoeck,
@ionferrico and others, to this paper by Leontidou et al where we describe our results from trying out a new type of commercial assay for #metabarcoding #microbial communities of several #16S hypervariable regions at once. Do check it out.
#MicrobialEcology #Molecular #Methods
https://ami-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16530
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling
"16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care"
https://www.biorxiv.org/content/10.1101/2023.11.07.564315v1
#metabarcoding #16S #rRNA #CopyNumber #bias #FunctionalInference #prediction
**Greengenes2 unifies microbial data in a single reference tree**
New resource harmonizes #16S and #shotgun #sequencing data for #microbiome research.
https://phys.org/news/2023-07-resource-harmonizes-16s-shotgun-sequencing.html
VertU: universal multilocus primer sets for eDNA metabarcoding of vertebrate diversity, evaluated by both artificial and natural cases
https://www.frontiersin.org/articles/10.3389/fevo.2023.1164206/full
#metabarcoding #vertebrate #primers #universal #16S #12S #COI
Does phylogeny explain bias in quantitative DNA metabarcoding?
https://mbmg.pensoft.net/article/101266/
#metabarcoding #phylogeny #quantification #16S #COI
"**Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses"**
#16S #metabarcoding #MarkerGeneSequencing #CopyNumber #Diversity #MicrobialDiversity #Bacteria #GeneCopyNumber
https://www.nature.com/articles/s43705-023-00266-0
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
"A comparison between Greengenes, SILVA, RDP, and NCBI reference databases in four published microbiota datasets"
https://www.biorxiv.org/content/10.1101/2023.04.12.535864v1
#16S #metabarcoding #MarkerGeneSequencing #SequenceDatabase #db #Greengenes #SILVA #RDP #NCBI #microbiome
Pack your bags folks, it's decided. /s #chatgpt3 #16S #metagenomics
