Daniel Baker

Aug 20, 2024 | biorxiv.org | Christopher Saunders |James Holt |Daniel Baker |Jonathan Belyeu

AbstractMotivation Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accuracy, long-read sequencing can substantially improve SV characterization when coupled with effective calling methods. While state-of the-art long-read SV callers are highly accurate, further improvements are achievable by systematically modeling local haplotypes during SV discovery and genotyping.

Apr 24, 2024 | biorxiv.org | Xiao Chen |Daniel Baker |Egor Dolzhenko |Joseph Devaney

AbstractVariant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of a gene family. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes. Analysis across five ancestral populations revealed highly variable copy numbers of these regions.

Jul 6, 2023 | genome.cshlp.org | Daniel Baker |Ben Langmead |Johns Hopkins

↵* Corresponding author; email: langmea{at}cs.jhu.edu Abstract A genomic sketch is a small, probabilistic representation of the set of k-mers in a sequencing dataset. Sketches are building blocks for large-scale analyses that consider similarities between many pairs of sequences or sequence collections. While existing tools can easily compare 10,000s of genomes, relevant datasets can reach millions of sequences and beyond.