We are big fans of #vg and obviously it was central to the work of this paper, hopefully that comes across! A shame we never quite managed to figure out getting SV allele frequency estimates from poolseq, but we are looking forward to genotyping SVs in individually sequenced samples in future!

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🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...

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Ever receive a BAM aligned to “GRCh38” and realize that could mean several different references? We just released ref-solver, a tool that identifies the reference genome behind BAM/CRAM/FASTA files by comparing sequence dictionaries to known builds. 🔗 whatsmygenome.fulcrumgenomics.com Read more 👇

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In the end @imartayan.bsky.social suggested to find a line starting with @ that is followed by a line not starting with @, which seems relatively nice, especially since these 2 are only separated by the header, so there's not too much back-and-forth scanning of (long) sequences.

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Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org. Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk! 💻🧬🦠🧫

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