A Galaxy-based bioinformatics project implementing the Vertebrate Genome Project (VGP) workflow to produce a haplotype-phased, chromosome-scale genome assembly from multi-platform sequencing data.
Organism: Saccharomyces cerevisiae S288C (Baker's Yeast)
Platform: Galaxy (usegalaxy.org)
Assembly strategy: HiFi + Hi-C + Bionano optical maps (VGP Trajectory D)
Data: Synthetic PacBio HiFi reads simulating a diploid yeast genome
The goal was to reconstruct both haplotypes of a diploid genome from scratch, validate quality at multiple checkpoints, and produce chromosome-level scaffolds — without relying on any reference genome during assembly.
| Technology | What It Contributes |
|---|---|
| PacBio HiFi | Long, accurate reads (10–25 kb, >99% accuracy) for contig assembly |
| Bionano optical maps | Mega-base scale physical information for ordering contigs |
| Illumina Hi-C | 3D chromatin contact data for chromosome-level scaffolding |
Each technology addresses a different limitation. HiFi reads span repetitive regions that short reads cannot resolve. Optical maps bridge gaps between distant contigs. Hi-C data anchors scaffolds to chromosome-scale structures.
HiFi reads (3 files)
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Cutadapt ──── Remove adapter-containing reads
│
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Meryl + GenomeScope2 ──── K-mer profiling → genome size & heterozygosity
│
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Hifiasm (Hi-C mode) ──── Phased contig assembly → Hap1 + Hap2
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QC checkpoint: gfastats / BUSCO / Merqury
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Bionano Hybrid Scaffold ──── Optical map integration
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BWA-MEM2 → YaHS ──── Hi-C scaffolding to chromosome level
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PretextMap / Pretext Snapshot ──── Final contact map visualisation
All datasets are publicly available on Zenodo.
| File | Format | Description |
|---|---|---|
| HiFi_synthetic_50x_01–03.fasta | FASTA | PacBio HiFi reads, 50x coverage |
| SRR7126301_1.fastq.gz | FASTQ.GZ | Hi-C forward reads |
| SRR7126301_2.fastq.gz | FASTQ.GZ | Hi-C reverse reads |
| bionano.cmap | CMAP | Bionano optical map |
Download links:
- HiFi: https://zenodo.org/record/6098306/
- Hi-C: https://zenodo.org/record/5550653/
- Bionano: https://zenodo.org/records/5887339/
| Tool | Version | Role |
|---|---|---|
| Cutadapt | 4.4 | Adapter removal |
| Meryl | 1.3 | K-mer counting |
| GenomeScope2 | 2.0 | Genome size estimation |
| Hifiasm | 0.19.8 | De novo phased assembly |
| gfastats | 1.3.6 | Assembly statistics |
| BUSCO | 5.5.0 | Gene completeness |
| Merqury | 1.3 | Quality value assessment |
| Bionano Hybrid Scaffold | 3.7.0 | Optical map scaffolding |
| BWA-MEM2 | 2.2.1 | Hi-C alignment |
| YaHS | 1.2a.2 | Chromosome scaffolding |
| PretextMap + Snapshot | 0.1.9 / 0.0.3 | Contact map generation |
Genome profile (GenomeScope2)
- Estimated haploid size: ~11.7 Mb
- Heterozygosity: 0.576%
- Coverage: ~50x diploid (~25x per haplotype)
Contig assembly (Hifiasm)
- Hap1: 16 contigs, ~11.3 Mb total
- Hap2: 17 contigs, ~12.2 Mb total
Final assembly
- 16 chromosome-level scaffolds (matches the expected yeast karyotype)
- High BUSCO completeness scores for both haplotypes
- Hi-C contact maps show clean diagonal banding consistent with correct chromosome assignment
.
├── README.md
├── workflow/
│ └── VGP_assembly.ga ← Importable Galaxy workflow
├── results/
│ ├── genomescope/ ← K-mer plots and summary files
│ ├── busco/ ← BUSCO bar charts (hap1 and hap2)
│ ├── merqury/ ← Spectra-CN and spectra-ASM plots
│ ├── gfastats/ ← Assembly statistics table
│ └── pretext/ ← Hi-C contact maps (before/after YaHS)
└── docs/
└── methods.md ← Detailed step-by-step methods
Requirements: A Galaxy account at usegalaxy.org or usegalaxy.eu with sufficient storage quota.
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Import the workflow — Go to Workflow → Import and upload
workflow/VGP_assembly.ga -
Upload input data — Add all six input files to your Galaxy history. Create a collection from the three HiFi FASTA files named
HiFi data. Rename the Hi-C files toHi-C_dataset_FandHi-C_dataset_R. -
Run — Go to Workflow → Run, select your inputs, and click Run Workflow.
For a full step-by-step walkthrough, follow the official Galaxy Training Network tutorial: https://gxy.io/GTN:T00039
Contig — A gapless sequence assembled directly from reads.
Scaffold — Contigs joined together with gap sequences (Ns).
N50 — The contig length at which 50% of the total assembly is covered.
Phasing — Separating reads/contigs into their correct haplotype of origin.
BUSCO — A benchmark measuring how many expected single-copy genes are present and complete.
Hi-C — A sequencing method that captures physical contacts between genomic regions in the nucleus.
- Rhie et al. (2021). Nature, 592, 737–746.
- Cheng et al. (2021). Nature Methods, 18, 170–175.
- Zhou et al. (2022). Bioinformatics, 39(1).
- Ranallo-Benavidez et al. (2020). Nature Communications, 11, 1432.
- Rhie et al. (2020). Genome Biology, 21, 245.
- Simão et al. (2015). Bioinformatics, 31(19), 3210–3212.