HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees

Abstract Premise Hybrid capture sequencing (Hyb‐Seq) is a widely used approach in phylogenomics, providing efficient access to targeted genomic regions. However, deriving high‐quality phylogenetic trees from raw sequencing reads requires extensive bioinformatics processing, which increases complexity, the risk of errors, and challenges in file management, especially for users unfamiliar with bioinformatics workflows. Methods and Results We developed HybSuite, a streamlined Bash‐based bioinformatics pipeline built upon mainstream tools such as HybPiper 2, designed to simplify the Hyb‐Seq phylogenomic analysis from raw reads to species trees. Compared to existing tools (e.g., HybPiper 2, CAPTUS), it offers a modular yet integrated workflow covering all key steps from downloading from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), adapter removal, data assembly, and paralog handling to species tree inference and extensive in‐depth analysis. We validated HybSuite by reconstructing a robust phylogeny for the Elaeagnaceae family, using the Angiosperms353 probe set and a dataset of 100 single‐copy nuclear loci from Arabidopsis . Conclusions HybSuite provides a flexible and user‐friendly pipeline for Hyb‐Seq phylogenomic analyses, and its high accuracy and efficiency were demonstrated through benchmarking with two empirical datasets. HybSuite is freely available at https://github.com/Yuxuanliu-HZAU/HybSuite . The pipeline is compatible with both the Linux and MacOS platforms.