vgp-pipeline
VGP Assembly Pipeline Skill
Overview
The Vertebrate Genome Project (VGP) assembly pipeline consists of Galaxy workflows for producing high-quality, phased, chromosome-level genome assemblies. This skill covers workflow selection, execution patterns, and quality control checkpoints.
Supporting files (detailed reference material):
- RESOURCE_ANALYSIS.md - Workflow canonical names, official/non-official filtering, metric availability, tool-level resource optimization
- DATA_INTEGRATION.md - ToLID patterns, GenomeArk S3 integration, NCBI accession recovery, Meryl k-mer management, species-metrics merging
- QUALITY_VALIDATION.md - Curation impact analysis, GenomeScope data validation, assembly size interpretation, communication patterns
Trajectories (by frequency of use)
Trajectory A: HiFi + Hi-C (Most Common)
- Inputs: HiFi Reads, Hi-C Reads
- Path: WF1 -> WF4 -> [WF6] -> WF8 -> WF9 -> PreCuration
- Output: HiC Phased assembly (hap1/hap2)
- WF6: Optional (can skip directly to WF8)
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