BLink-seq delivers population-scale haplotypes without long reads: a scalable framework for non-model genomics

BLink-seq is a linked-read sequencing library-preparation method that runs on standard short-read sequencers using low-cost reagents and scales to high-throughput sample processing. We tuned library-prep parameters against linked-read quality metrics, then tested phasing and structural-variant detection at two evolutionary extremes: an inbred Drosophila melanogaster cross carrying known inversions, and four wild-caught Atlantic silverside (Menidia menidia) parent-offspring trios. Applying the protocol across 376 silversides, we recovered chromosome-scale phased blocks, recovered the known inversions in both validation sets, and uncovered previously undescribed structural complexity inside an adaptive inversion on silverside chromosome 11.

Documentation and a user guide are available at blinkseq.github.io.