PhD student Data Science and Bioinformatics at the RKI in Berlin, Germany.
Berlin
Joined October 2010
- Tweets42
- Following225
- Followers61
- Likes72
1/6 🎉 Excited to announce WarpDemuX v0.4.4 with RNA004 support! Our (@PatrickBohnPB ) WDX4 model achieves 99.5% target accuracy with 95% yield on the latest RNA sequencing kit from @nanopore. Release notes at: github.com/KleistLab/WarpDem…
Wiep van der Toorn retweeted
It's Christmas in advance with a very special @nanopore #opendata release ! 🎅
Today we are releasing our 5mC 5hmC and 6mA DNA mod synthetic control datasets with each mods in all possible 5 mers contexts. All nicely wrapped in a comprehensive validation blog post.🎁
New blog: Modified Base Best Practices & Benchmarking for @nanopore 🧬 sequencing Includes:
* Raw POD5 files for synthetic ground truth strands
* Modified base calling best practices
* Modkit recommendations
Check it out: labs.epi2me.io/mod-validatio… #methylation #bioinformatics
Wiep van der Toorn retweeted
VERY excited to share SeqTagger with the world! If you want to learn more about our super-fast and accurate demultiplexing tool for direct RNA-sequencing (DRS), check out the thread below. bit.ly/3ClVYxG (1/15) 🧵
Extremely excited to share that our Nanopore direct RNA multiplexing solution--WarpDemuX, is here!
WarpDemuX is both fast and highly accurate. Check out @PatrickBohnPB's awesome thread on our work! 👇
Finally, meet WarpDemuX!
Our (@wiepp) solution for dRNA multiplexing - so fast it runs on any laptop, and so accurate that we could demux even super low abundance samples with high specificity!
And imho the coolest thing? We've also run dRNA live barcode balancing with it 👀
For those interested, WarpDemuX and its models, including one trained on DeePlexiCon barcodes, are available for use. Dive into our preprint for all the details. 🚀🔬
biorxiv.org/content/10.1101/…
Wiep van der Toorn retweeted
#INSPIEsVigilanciaGenómica
Técnicos e Investigadores del INSPI @Salud_Ec @AgrocalidadEC y @Ambiente_Ec fortalecen sus conocimientos en Vigilancia Genómica ante posibles brotes de epidemias de Influenza Aviar en el Ecuador.
Leer más ➡️bitly.ws/JbAm
Wiep van der Toorn retweeted
#INSPIVigilanciaGenómica
INSPI @ABG_galapagos @AgrocalidadEC y @Ambiente_Ec participan en taller “Secuenciación de Nueva Generación y Bioinformática” organizado por @giz_gmbh para ampliar las capacidades técnicas en la Caracterización y Vigilancia Genómica de la Influenza Aviar.
Wiep van der Toorn retweeted
Overall, C is the least accurate nucleotide, but sequence contexts matter greatly! The most accurate 3-mer context “GCA” shows clear signal-level separation with its mismatched motif "GUA", while the worst “UCU” is almost identical to “UUU”… 2/3
Wiep van der Toorn retweeted
Looking forward to the direct RNA update tomorrow #nanoporeconf! Meanwhile, we also updated our preprint on dRNA-seq systematic errors with signal analysis, first is the mismatch error relationship between the 4 bases and their signal features (esp. intensity and dwell time) 1/3
Wiep van der Toorn retweeted
Pleased to be able to contribute here; study led by Max v Kleist (@rki_de @FU_Berlin) & Redmond Smyth lab (@Helmholtz_HIRI).
Updated preprint: biorxiv.org/content/10.1101/…
Liuwei (@ChaseLiuweiWang) & Wiep (@wiepp) are at London Calling in person #nanoporeconf; go talk to them! 3/3