Bioinformatic pipeline underlying the analyses of RADseq data of Siberian taimen (Hucho taimen)

The workflow documents demultiplexing, read filtering, mapping to the Hucho hucho reference genome, duplicate marking, joint SNP calling with FreeBayes, SNP-level quality filtering with VCFtools and dDocent/Puritz filters, HWE-based quality control, phylogenomic tree reconstruction, removal of technical replicates, individual-level missingness assessment, rCNV-based filtering of putative paralogous or copy-number-variable loci, and final biallelic SNP filtering.

The pipeline produces the final SNP dataset of 36,194 biallelic SNPs used for downstream population genomic analyses. All analyses were run on a Linux machine running Ubuntu Server with 128 GB RAM and an AMD AM4 CPU Ryzen 9 5900X 3.7GHz 70MB Cache processor.