Kind of nuts that one can make all of these cards for offloading with clang (AMD requires cosplaying as a different architecture) via @openmp_arb
True performance portability
#GPU #openmp
Time to try slorado now #RNAseq!
https://www.amd.com/en/blogs/2025/breaking-barriers-in-genomics.html
https://www.biorxiv.org/content/10.64898/2026.03.25.714356v1
Pipeline release! nf-core/rnafusion v4.1.2 - 4.1.2!
RNA-seq analysis pipeline for detection of gene-fusions
Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/4.1.2
#fusion #fusiongenes #genefusion #rna #rnaseq #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/rnafusion v4.1.1 - 4.1.1!
RNA-seq analysis pipeline for detection of gene-fusions
Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/4.1.1
#fusion #fusiongenes #genefusion #rna #rnaseq #nfcore #openscience #nextflow #bioinformatics
StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts
Accurate assembly of rRNA-depleted (total) RNA sequencing (RNA-seq) remains challenging because existing methods often conflate incomplete, nascent RNA with fully processed mature isoforms, leading to misassemblies and quantification errors. Here, we present StringTie3, a major update to the widely used StringTie assembler, specifically designed for total RNA-seq. StringTie3 introduces a nascent mode that models co-transcriptional splicing to separate nascent from mature transcripts, and a refined long-read module that distinguishes genuine polyadenylation sites from poly(A)-priming artifacts. Across short-, long- and hybrid-read datasets, StringTie3 substantially reduces assembly errors and outperforms existing tools. In Argonaute knockout experiments, nascent-mode analysis reveals that single knockouts predominantly alter nascent transcripts while leaving mature RNA largely unchanged, whereas double or triple knockouts disrupt both fractions. In breast cancer samples, certain extracellular matrix and tumor suppressor genes show discordant nascent and mature expression, suggesting posttranscriptional regulation. StringTie3 provides a framework for investigating transcriptional and posttranscriptional processes in total RNA-seq data. StringTie3 shows enhanced performance in total RNA-seq assembly and quantification by modeling both nascent and mature transcripts, across short-, long- and hybrid-read sequencing data.
Low-hanging fruit: everyone sees it, few actually pick it up ๐๐๐๐๐ซ๐
Our latest preprint explores dark pigmentation in blackberry, a plant characterized by low-hanging fruit. The combination of genomics and transcriptomics reveals insights into the genetics of pigment biosynthesis. High levels of cyanidin-3-O-glucoside were identified in blackberries, which may explain their dark coloration.
Read more: https://doi.org/10.64898/2026.05.05.723051
#PlantSciences #Pigments #Fruits #Genomics #RNAseq
@PuckerLab
Pipeline release! nf-core/rnaseq v3.26.0 - nf-core/rnaseq v3.26.0 - Chromium Cuttlefish!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.26.0
RE: https://mstdn.science/@nf_core/116460527673313236
kudos to my internship student who added stringtie_merge to the workflow. ๐ฅณ
Pipeline release! nf-core/rnaseq v3.25.0 - nf-core/rnaseq v3.25.0 - Plutonium Pangolin!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.25.0
Ming 'Tommy' Tang
Christos Argyropoulos MD PhD
Christos Argyropoulos MD, PhD, FASN ๐บ๐ธ 0kale/acc
nf-core
Pierre Lindenbaum
Boas Pucker