Tumamoca (GlobeBerry) Genome Assembly

Overview

This repository contains scripts, configuration files, and summary results used to assemble and evaluate the Tumamoca (GlobeBerry) genome using PacBio HiFi and Hi-C data. The goal is to produce a high-quality, reproducible reference assembly suitable for downstream comparative genomics, conservation genetics, and functional studies.

What’s in this repo

• Reproducible command logs and scripts for each assembly stage
• Assembly evaluation outputs (e.g., BUSCO/QUAST/Merqury summaries)
• Documentation describing design choices and known issues

Note: Large raw data and bulky outputs (FASTQ/BAM/FASTA intermediates) are intentionally not tracked in git. This repo focuses on code + configs + lightweight summaries.

Data types

• PacBio HiFi reads (primary assembly input)
• Hi-C read pairs (scaffolding / validation)
• Ultima reads (validation)

High-level workflow

1. QC & read stats
2. Primary HiFi assembly (hifiasm)
3. Organelle/contaminant filtering (using oatk)
4. Hi-C scaffolding (HapHiC)
5. Polishing / curation (racon)
6. Assembly evaluation
   • BUSCO completeness
   • QUAST assembly metrics
   • Merqury k-mer completeness