hybpiper-rbgv

hybpiper-rbgv assembles target enrichment (sequence capture) data and identifies paralogs to infer ortholog groups from gene tree topologies for phylogenomic analyses, including studies of non-model organisms without a known species tree.

Key Features:

• Target-enrichment assembly: Assembles target enrichment (sequence capture) data with options for handling supercontigs.
• Paralog identification and orthology inference: Identifies paralogs and infers ortholog groups using gene tree topologies and the Yang and Smith method.
• Improved HybPiper scripts: Includes updated scripts and bug fixes with novel options to integrate supercontig handling and ortholog-group inference.
• Nextflow workflows: Implements the pipeline as two Nextflow workflows to manage analysis steps.
• Containerization: Provides a Singularity container for consistent software environments.
• Testing with datasets: Has been tested with several datasets, including a demonstration dataset.

Scientific Applications:

• Phylogenomic assembly: Assembly of target enrichment data for phylogenomic datasets.
• Orthology and paralogy analysis: Inference of ortholog groups and detection of paralogs to support accurate evolutionary inference from gene trees.
• Non-model organism studies: Application to phylogenomic studies of non-model taxa where a species tree may be unavailable.
• Large-scale phylogenomic projects: Use in large-scale projects such as the Australian Angiosperm Tree of Life project.

Methodology:

Assembles target enrichment (sequence capture) data; updated HybPiper scripts add supercontig handling; identifies paralogs and infers ortholog groups from gene tree topologies using the Yang and Smith method; implemented as two Nextflow workflows and distributed via a Singularity container; tested on multiple datasets.