TrendBio

#32 · ML / AI methods

Locus-resolved tools scale variant interaction, colocalisation and SV detection

1 preprint · 2 published
Items per day, last 8 weekstoday: 3

Most items here are computational tools, and the common thread is locus-resolved analysis of genomic variation. GWAIS-Web performs genome-wide SNP-SNP interaction screening in case-control GWAS with GPU/FPGA acceleration, and gpu-coloc reports a roughly 1000-fold speedup for genetic colocalisation across millions of association signals. GrassSV combines depth-of-coverage and contig-based recognition to detect major structural variant classes from high-throughput DNA-seq data. Aardvark adds a basepair score for haplotype comparison, reducing representation bias for small variants. ReSeT selects reference genomes using a facility-location objective with an inter-taxon discrimination term and an ambiguity index, benchmarked on viral datasets. What is new is the extension of locus-resolved analysis to pairwise interaction and colocalisation at million-scale, alongside benchmarking of variant representation.

Published papers

Preprints

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