🛠️ Resources

All code, datasets, and reproducible pipelines are openly available: github.com/alihamraoui/...

#bioinformatics #RNAseq #singlecell #alternativesplicing #benchmark #opensource #scRNAseq #MinION

cc @fr-genomics.bsky.social @mthomaschollier.bsky.social

🤝 Why it matters

Understanding isoform diversity at the single-cell level is crucial for uncovering novel regulatory mechanisms.
Our benchmark serves as a reference point for researchers selecting appropriate tools and workflows.

✨ Key findings

Accurate isoform quantification remains challenging, with variability across protocols and methods.

Some pipelines handle UMIs and barcodes more efficiently, improving isoform detection.

We provide best practice recommendations and a fully reproducible framework for future studies.

dedicated to resolving alternative splicing at single-cell resolution.

The evaluation spans 10 state-of-the-art methods, tested across simulated and real @10xgenomics.bsky.social datasets sequenced on multiple #illumina and @nanoporetech.com platforms.

🚀 Our new preprint is now live on bioRxiv!
“A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data”
🔗 Read here: www.biorxiv.org/content/10.1...

🔬 About the study
We present the first comprehensive benchmark of bioinformatics tools 👇

🎉 Our core facility has just renewed its certifications ISO 9001 and NFX-50-900 ! These certifications are particularly important with regards to our users, but also as we are member of @fr-genomics.bsky.social.

#AsaruSim is a flexible and efficient tool to simulate single-cell and spatial long-read RNA sequencing data.

#AsaruSim is part of our upcoming efforts to benchmark state-of-the-art single-cell and spatial Nanopore long-read sequencing methods. Stay tuned for the results in the upcoming weeks…

For our 1st post on Bluesky, we are excited to announce the publication of our new #bioinformatics tool #Asarusim for #SingleCellRNAseq coupled with @nanoporetech.com sequencing ! 🎉 🎊
👉 article : academic.oup.com/bioinformati...
👉 GitHub : github.com/GenomiqueENS...

cc @fr-genomics.bsky.social