Ryan Layer
@ryanlayer.bsky.social
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Making genomics faster layerlab.org
reposted by
Ryan Layer
Nature Computational Science
12 months ago
📢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
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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.
https://www.nature.com/articles/s43588-024-00763-9?utm_source=bluesky&utm_medium=social&utm_campaign=natcomputsci
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We have preprint GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts led by Kristen Schneider (who defended!)that can search +70k samples in the Campus Colorado Center for Personalized Medicine biobank in <1 sec
www.biorxiv.org/content/10.1...
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GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts
Many patients do not experience optimal benefits from medical advances because clinical research does not adequately represent them. While the diversity of biomedical research cohorts is improving, en...
https://www.biorxiv.org/content/10.1101/2024.11.02.621671v1
about 1 year ago
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reposted by
Ryan Layer
Stephen Turner
about 1 year ago
STABIX: Summary statistic-based GWAS indexing and compression
https://www.biorxiv.org/content/10.1101/2024.11.15.623812v1.full
🧬🖥️🧪
https://github.com/kristen-schneider/stabix
from
@ryanlayer.bsky.social
lab
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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...
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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...
https://www.biorxiv.org/content/10.1101/2024.11.15.623812v1
about 1 year ago
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