HybPiper

HybPiper extracts target gene sequences from high-throughput DNA sequencing reads to enable targeted sequence-capture analyses for phylogenetic reconstruction.

Key Features:

• Targeted Sequence Capture: Enriches and recovers specific gene regions from targeted-enrichment sequencing datasets for downstream phylogenetic analysis.
• Integration with Bioinformatics Tools: Implements a collection of Python scripts that act as a wrapper to connect and run existing bioinformatics tools for sequence extraction and assembly.
• Optimization for Degraded DNA: Handles short sequences derived from degraded DNA, including museum and herbarium specimens, during assembly and recovery of targets.
• Incorporation of Flanking Non-coding Sequences: Retains and extracts flanking non-coding regions in addition to coding targets to increase gene-tree resolution.
• Handling Paralogous Loci and Off-target Sequences: Identifies and addresses issues related to assembly, paralogous loci, partitions, and off-target sequences to support robust phylogenetic inference.

Scientific Applications:

• Artocarpus (Moraceae) phylogeny: Enabled construction of a 517-gene phylogenetic framework with 96% taxon sampling using both recent field-collected and herbarium specimens up to 106 years old, where inclusion of non-coding sequences improved gene tree resolution.

Methodology:

A collection of Python scripts that wrap and integrate existing bioinformatics tools to extract targets and optimize assembly for targeted-enrichment sequence data, including handling short reads from degraded DNA, identifying paralogous loci and off-target sequences, and increasing dataset sizes to address gene-tree conflict.