Genomic Overview
This research project utilizes PacBio HiFi (Long-Read) technology to reconstruct the complex eukaryotic genome of Oryza sativa. Rice is a critical model organism in plant biology, and high-quality de novo assemblies are essential for understanding climate adaptation and yield optimization.
K-mer Profiling (Jellyfish)
Before assembly, we performed k-mer counting to estimate the genome size and check for heterozygosity. This step ensures the data quality is sufficient for Hifiasm.
Figure 1: Estimated k-mer frequency distribution (Waiting for HPC processing results).
Primary Assembly Metrics
| Metric Type | Target Specification |
|---|---|
| Expected Genome Size | ~370 - 400 Mb |
| Contiguity (N50) | High (Optimized by Hifiasm) |
| Scaffolding Method | Reference-guided (RagTag / IRGSP-1.0) |
| Organelle Genomes | Separated (Chloroplast & Mitochondrion) |