TY - JOUR AU - Casanova, Adrián AU - Maroso, Francesco AU - Blanco, Andrés AU - Hermida, Miguel AU - Ríos, Néstor AU - García, Graciela AU - Manuzzi, Alice AU - Zane, Lorenzo AU - Verissimo, Ana AU - García-Marín, José-Luís AU - Bouza, Carmen AU - Vera, Manuel AU - Martínez, Paulino PY - 2021 DA - 2021/03/02 TI - Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species JO - BMC Genomics SP - 150 VL - 22 IS - 1 AB - The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. SN - 1471-2164 UR - https://doi.org/10.1186/s12864-021-07465-w DO - 10.1186/s12864-021-07465-w ID - Casanova2021 ER -