Biologically inspired graphs to explore massive genetic datasets - Nature Computational Science
A recent study proposes a data structure that addresses crucial challenges related to storage and computation of large genome databases.
📢In a recent News & Views, @ryanlayer.bsky.social discusses a data structure introduced by @aprilwei.bsky.social and colleagues for reducing storage and computational costs for phased whole-genome polymorphisms. www.nature.com/articles/s43...
🔓https://rdcu.be/d8ay3
31.01.2025 13:56 — 👍 6 🔁 2 💬 0 📌 1
STABIX: Summary statistic-based GWAS indexing and compression
Genome-Wide Association Studies (GWAS) are widely used to investigate the role of genetics in disease traits, but the resulting file sizes from these studies are large, posing barriers to efficient st...
We have a method for fast GWAS data access. STABIX adds a p-value index that with a position index (what TABIX has) allows you to quickly retrieve, eg. all significant SNPs in a target gene. Also column compression to reduce the size. www.biorxiv.org/content/10.1...
github.com/kristen-schn...
21.11.2024 15:11 — 👍 16 🔁 5 💬 0 📌 0
Associate Professor @ UC-Davis | Former Senior Director @ Exai Bio | Computational Biology, ML/AI, Genomics, RNA, Cancer
Dad, bioinformatician, ex-expat. Currently working on transposon bioinformatics & infectious disease genomics.
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