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
Probably the most complete snail genome yet, a chromosome-level assembly for the aptly-named, invasive 'Asian Tramp Snail' *Bradybaena similaris. *This particular one was not difficult - but it has been a long road to get to this point. #genomics #snails #HiFi #PacBio Link now added: https://academic.oup.com/gbe/article/17/5/evaf070/8112707
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
Posted on #Aseq #NGS #DNASequencing #Illumina #PacBio
I've been reviewing state of ONT & PacBio #Archaea raw data availability in public repos (preprint coming soon). It's not fantastic.
Once we upload current reads, our warehouse & partner lab might be THE top uploader in the world in terms of diversity of Archaeal species contribution.
We're also covering both #ONT and #PacBio for each species - so 2x the count.
I'll also upload all ONT raws in blow5 format as well! Down with vendor lock-in.
Pipeline release! nf-core/pacvar v1.0.1 - v1.0.1 - Sardine [3/6/2025]!
Please see the changelog: https://github.com/nf-core/pacvar/releases/tag/1.0.1
#alignment #longread #pacbio #puretarget #variantcalling #wgs #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/pacvar vv1.0.0 - nf-core/pacvarv1.0.0 - Goldfish [2/05/2024]!
Please see the changelog: https://github.com/nf-core/pacvar/releases/tag/v1.0.0
#alignment #longread #pacbio #puretarget #variantcalling #wgs #nfcore #openscience #nextflow #bioinformatics
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
🚀 We’ve just kicked off another edition of our Eukaryotic Genome Assembly using @PacBio and Hi-C data course! Thrilled to have a great group of international attendees diving deep into genome assembly with Marcela
& Joao! 🌍🧬 #GenomeAssembly #PacBio
I have a big microbial sequencing batch coming up that will require decent methylation calling.
How's ONT vs PacBio on this front? R10's direct methylation detection is exactly what I'm looking for, but curious about first-hand experience from researchers for both platforms.
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
Sequencing Life To Conserve Biodiversity
Neil Ward tells us about the role that genomics can play in conserving biodiversity and how innovative technologies such as HiFi sequencing are helping biodiversity projects. #pacbio #hifisequencing #genomics #biodiversity #conservation #science #darwinproject #technology #conservative
https://www.technologynetworks.com/tn/blog/sequencing-life-to-conserve-biodiversity-385960
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
minimap2-rs updated! Now using minimap 2.27. Needletail + rayon support! Thanks for all the pull requests to help get this here!
https://crates.io/crates/minimap2
All changes: https://github.com/jguhlin/minimap2-rs/?tab=readme-ov-file#0117-minimap2-227
#rust #bioinformatics #genomics #nanopore #pacbio #RustLang
Well, sometimes I feel like I'm playing Doom on a "nightmare" difficulty level.
4 species, 2 types of long reads data, 3 different assemblers.
6 assemblies crashed, 4 GitHub issues filled (2 postponed), 2 fixed, 1 more - workaround found, 1 - no repy.
Restarted assemblies, got 2 more crashes.
This is not going to end soon.
Okay, hive-mind: what tools are people using to #assemble older (non-HiFi) #pacbio reads? I seem to remember hearing someone say that pre-filtering of reads can make assembly more tractable, but I might be entirely mistaken here? Is there some way to make these older reads compatible with the #HiFi assemblers? #genomics #GenomeAssembly #LongReads
Digging through some old #pacbio data from 2015. A quick way to handle bax files from back then seems to be bax2bam off conda - but the latest version (2 years old) has a weird bug that's never been fixed.
If you're getting read quality metrics error during conversion, try bax2bam=0.0.9 installation instead.
Not liking the idea of deprecated proprietary binary data in public (NCBI) databases :/ #bioinformatics
Woohoo!! Just won a small pilot grant to use #longReads for #scRNAseq in #RheumatoideArthritis !
#nanopore vs #pacBio...
