Metagroup of labs working with population, medical, statistical, and conservation genetics at @uni_copenhagen
Copenhagen, Denmark
Joined March 2021
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🧵1/5 🧬New paper out!
We present the first whole-genome data for the giant forest hog, #Hylochoerus #meinertzhageni (GFH), filling a major gap in our understanding of African #suid #evolution.
📖 Read the paper in iScience: doi.org/10.1016/j.isci.2026.…
#Genomics #Conservation
🧵5/5 The GFH is currently listed as “Least Concern,” but these findings highlight the deep evolutionary structure within the giant forest hog and have important implications for its conservation. Further research and reassessment of the GFH status is needed 🐗🧬
This work was led by @MartaCiucani, with contributions from the group and collaborators. We thank everyone involved in making this study possible, including PIs @idamoltke, @A_Albrechtsen & @HellerRasmus 🐗🧬
🧵1/2 AdapterRemoval v3, a dang fast(Q) processor, is here! 🚀
AdapterRemoval v3 filters and trims high-throughput sequencing data, merges overlapping reads, performs demultiplexing, & generates detailed QC reports (HTML & JSON), and does so much faster than #AdapterRemoval v2.
🧵2/2 New features in #AdapterRemoval v3 include QC reports, automatic adapter selection, improved demultiplexing, new trimming/filtering algorithms, automatic poly-G trimming, flexible output merging, SAM/BAM output, Windows support and more:
github.com/MikkelSchubert/ad…
🧵1/5
Thought long-read sequencing had “solved” structural variant genotyping? We did. Turns out many SVs still have high genotype error rates with current tools. Our new method SVUPP uses long-read pre-phasing to reduce errors and improve genotype quality
doi.org/10.1093/bioinformati…
🧵4/5
Limitation: all SV genotype callers perform poorly for SVs with neighbors (>20% error), which make up ~40% of SVs. Our results apply to the remaining 60%. If SVs with neighbors are important to your analysis, HiFi data + kanpig is currently the least-bad option.
🧵5/5
The paper is first-authored jointly by @zilongli21 and @ffstaeger and recently published in Bioinformatics. This method is designed for single sample SV genotyping. Stay tuned for population-level joint SV genotyping!
Big science highlights this month at our #EPIC seminar! Kees uncovered new insights into isolation by distance and shorebird diversity🐧, and Anna showed how ancient chewing gums provide a remarkable snapshot into #microbiome 🦠evolution and health. Fascinating work from both! 👏
Our new paper on Indonesian cattle #genomics is out on @NatureComms 🎉
Did you know Indonesian #cattle 🐂 were a mix of two species?
Great work: @XiWang91099530 @sagitaninta @HellerRasmus @casia16
Read 👉 nature.com/articles/s41467-0…
#popgen #evolution
🧵
🧵 The potential of new unique variants that can improve cattle productivity via genomic selection, making them high yield while being adaptive to hot climate, and potentially breed environmentally friendly cattle with low carbon footprint.