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

Résumé fourni par la source

Bioinformatic pipeline for processing Siberian taimen (Hucho taimen) single-digest RADseq data. 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.

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