AmpliRAD: A new method combining amplicon and RAD sequencing

This dataset provides the genomic data and computational framework
supporting the development and validation of AmpliRAD, a novel sequencing
method that integrates targeted amplicon sequencing with a genome-wide
reduced-representation (RAD-seq) approach. The data was generated to
demonstrate a streamlined workflow that enables simultaneous analysis of
specific adaptive markers and broad population structure in non-model
organisms. A primary focus of the dataset is the technical evaluation of
the AmpliRAD method, including a direct comparison of sequencing yields
and target enrichment success against samples processed using a
traditional RAD-seq protocol. These comparative metrics include read
counts mapping to target regions and the assessment of coverage evenness
across 39 target loci, providing a benchmark for the method's
efficiency. Additionally, the dataset includes genomic information from 96
Chinook salmon (Oncorhynchus tshawytscha) collected from the Dean River,
British Columbia, including 55 adults and 41 juveniles. These data include
targeted genotypes for SNPs on chromosome 28 associated with adult
migration timing—specifically within the GREB1L region—as well as a panel
of over 31,000 RAD-seq SNPs used to assess fine-scale population
structure. Researchers can reuse this dataset as a template for
implementing analysis of AmpliRAD data in other species or to explore the
genetic basis of migration timing in northern salmon populations. While
many different approaches could be used to analyze AmpliRAD data, the
included bioinformatics pipeline offers a complete path from raw reads to
population structure analysis, designed to be accessible to researchers
seeking cost-effective genomic tools.