Live and recent posts from across the Fediverse tagged #radseq, aggregated by home.social.
🤗🤗🤗 We welcome Moritz Kahnert @Mol_Ecol @uniinnsbruck !
For his master thesis, he explores how hemeroby influences the population genomics and trophic ecology of the firebug
https://molecular-ecology.at/moritz-kahnert/
#biodiversity #ecology #conservation #UrbanEcology #RADseq #Pyrrhocoris
rsx: Rust rewrite of the RADSex command set. Same marker tables. Memory bound is the number of individuals. Each marker is a strict call, a posterior-supported hypothesis, or a Bayes-factor-only row.
8.38x geometric-mean faster across 56 pairs on 41.9 billion bases. CUDA up to 29.86x on the p-value batch.
https://doi.org/10.1186/s12859-026-06628-4
https://rsx.rgoswami.me
🚀 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!
Fretting over my RADseq data with 30,000 loci...wondering why gene diversity is so skewed. Boxplot shows distribution across loci. Typical for #RADseq? Or a sign of bad data?
#PopulationGenetics
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
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:
🥁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/
Cool new study that quantifies sample cross-contamination, including laboratory mitigation methods: https://doi.org/10.1093/icesjms/fsad004
#genomics #genetics #GBS #RADseq #fisheries #tuna #fieldwork #marinesci #marinebio #ecology #conservation
To get the ball rolling, I'd like to share a recent paper! Genotyping-by-sequencing for biogeography: https://doi.org/10.1111/jbi.14516
We provide a practical guide for #biogeography using #GBS or #RADseq, which should particularly assist new users or students. There's a wealth of research exploring differences in reduced-representation sequencing (RRS) methods, sources of genotyping error, and much more. Our aim was to guide new users through this exciting literature. #genomics #ecology #evolution #DNA
Curious how folks might explain this PCA generated from RADseq population genetic data. Something's explaining 97.9% of the variation--but what?? Its not revealing any pattern!
"Fig 4. Principal components analysis on the genotypes for 55 D. elator samples (historical and contemporary) using the dudi.pca function in R package ‘adegenet’.
While there are no clear clusters emerging on PC1, geographic location seems to correspond with PC2."
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0274554
#PopulationGenetics
#RADseq
Sitting here staring at the terminal window waiting very impatiently for my #RADseq analysis to finish. This is my second library (the first enzyme combo produced too many fragments). If this one fails, I'm doomed as there's no more $$ for a third try.
It's for #ConservationGenetics of the #CrawfishFrog. They're counting on me 😭
PhD position available at Lund University on conservation genomics of orchids in Sweden. Apply here: https://lu.varbi.com/en/what:job/jobID:557391/type:job/where:4/apply:1