HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

Abstract

Summary:Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of “quality-filtered” genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes.Availability:The HybPhyloMaker scripts, manual as well as a test data set, are available in https://github.com/tomas-fer/HybPhyloMaker/. HybPhyloMaker is licensed under open-source license GPL v.3 allowing further modifications.

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomicticRanunculus auricomuscomplex (Ranunculaceae)

“…Two different paired-end sequencing runs (2x 250 bp) were performed on an Illumina MiSeq System (Illumina Inc., San Diego, USA). The obtained raw reads were processed using the pipeline HybPhyloMaker (all scripts available at: https://github.com/tomas-fer/HybPhyloMaker/; Fér and Schmickl (2018). Before analyses, reads were phased using SAMtools vers.…”

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

“…for the pipeline with details of data preparation and analyses. A combination of HybPhyloMaker (Fér and Schmickl, ) and HybPiper (Johnson et al., ) was used for data preparation and analyses in the following sections. The first steps in data preparation for each sample were conducted in HybPhyloMaker, a pipeline that makes use of already available software (see details below) to perform Hyb‐Seq data analyses.…”

“…). The single reference file for read mapping in HybPiper contained all reference sequences for each of the 1061 reference loci; read mapping was conducted using BWA, and contig assembly was performed using SPAdes in HybPiper (see Fér and Schmickl [] for further comparisons between HybPiper and HybPhyloMaker). Paralogous loci were flagged in HybPiper using the following (default) settings: multiple long‐length contigs (>85% of the reference locus) with similar coverage (within 10× of each other) that mapped to a reference locus.…”

Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above

“…Lemmon & Lemmon, ; Barrett et al ., ) and generally demands less complex bioinformatics (e.g. Fér & Schmickl, ). Reduced representation techniques such as restriction site‐associated DNA sequencing (RADseq, Baird et al ., ) or genotype‐by‐sequencing (Elshire et al ., ) work well for population‐level analysis and do not require a reference genome.…”