🚀 New bash pipeline for #ddRADseq preprocessing & deduplication!
✔️ Adapter trimming
✔️ Barcode demux
✔️ Cut site filtering
✔️ Pairwise dedup (w/ seqtk + awk)
✔️ Reproducible + lightweight

📂 GitHub: https://github.com/rafalwoycicki/ddRADseq_reads

🔁 RTs & feedback welcome! #bioinformatics #RADseq

🚀 New bash pipeline for #ddRADseq preprocessing & deduplication!
✔️ Adapter trimming
✔️ Barcode demux
✔️ Cut site filtering
✔️ Pairwise dedup (w/ seqtk + awk)
✔️ Reproducible + lightweight

📂 GitHub: https://github.com/rafalwoycicki/ddRADseq_reads

🔁 RTs & feedback welcome! #bioinformatics #RADseq

At the end of a long day of #bioinformatics I've confirmed that I can cut my sequencing depth by half in the next round of sampling. Which means costs drop by half as well!

By tomorrow we'll see if we can cut by another half again.

Motivated by wanting to do #RADseq / #GBS population #genetics work on an octoploid plant. ugh!

🚨Very happy to inform you that our #RADseq course is back!

‼️🚀Save the date and join us in November to learn how to analyse your RADseq data with this stellar team of instructors @naiara_re @TerezaManousaki and @NataliaDA10 🤩

✏️https://physalia-courses.org/courses-workshops/course16/
@RAD_seq

🚨 Ready to master #RADseq data analysis with #Stacks? Join our course led by the amazing @naiara_re, @TerezaManousaki, and @NataliaDA10!

👉 Grab your spot here – only a few seats left! ⏳
https://www.physalia-courses.org/courses-workshops/course16/

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians
Loïs Rancilhac et al.
bioRxiv 2023.04.19.537466; doi: https://doi.org/10.1101/2023.04.19.537466

#RADseq #phylogenetics

What is the key element in a successful #RADseq experiment and analysis? How can you avoid the dreaded "missing data"?

tldr; it's the quality of input DNA, and controlling the resulting levels of PCR duplicates that matters.

Our latest work, led by Nicolas Rochette and Angel Rivera-Colón, (and in collaboration with Shane Campbell-Staton and Floragenex) shows this in great detail via modeling and experimental analysis. Now published in Molecular Ecology Resources:

https://doi.org/10.1111/1755-0998.13800

🥁Registration is now open for the next edition of the #RADseq #dataanalysis course with @naiara_re @TerezaManousaki & @NataliaDA10

Have a look at it: https://physalia-courses.org/courses-workshops/course16/

#bioinformatics #genomics