Arda Söylev

gaftools provides utilities for processing graph alignments in GAF format, adapting SAMtools functionalities for pangenome analysis.

The paper introduces synteny-aware pangenome graphs to visualize genomic variation in marine bacteria, revealing structured continua of variability across genomes.

The paper uses long-read sequencing to characterize structural variants in 1,019 samples from the 1000 Genomes Project, identifying 167,291 sequence-resolved SVs and highlighting their genomic and functional implications.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

SVarp discovers haplotype-resolved structural variants using a pangenome reference and long reads, achieving high recall in simulated and real data.

CONGA genotypes copy number variants in ancient genomes and low-coverage data, showing coherent deletion frequencies and purifying selection across 50 ancient human genomes.

MTaxi classifies closely related species from low coverage ancient DNA data using mitochondrial DNA substitutions, achieving 100% accuracy on tested samples.

This study benchmarks WGS-based structural variant callers using a PCR-confirmed gold standard, finding wide performance variation and identifying tools best suited for low and ultra-low pass data.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper develops TARDIS, a tool for accurately detecting complex structural variations, including tandem and interspersed segmental duplications, using short-read whole genome sequencing data.