oryza-sativa-genome-assembly

Advanced plant genome assembly pipeline for Oryza sativa using HiFi reads, k-mer profiling (Jellyfish), and Hifiasm

Plant Genome Assembly: Oryza sativa (Rice)

This repository contains a high-performance bioinformatics pipeline for assembling the Oryza sativa genome using PacBio HiFi reads (Accession: SRR35146894).

Project Features

Compared to bacterial assembly, this project handles a larger eukaryotic genome, requiring advanced k-mer profiling and specialized assemblers for long reads.

Key Components:

• Data Retrieval: Automated SRA data download via sra-tools.
• K-mer Profiling (Jellyfish): Multi-k analysis (k=21, 51) to estimate genome size, heterozygosity, and repeat content.
• Long-read Assembly (Hifiasm): State-of-the-art assembler specifically designed for PacBio HiFi reads.
• HPC Optimized: Configured for multi-threading (up to 20 threads) and memory-intensive processing.

Pipeline Workflow

1. Setup: Workspace initialization.
2. K-mer Counting: Generating histograms with jellyfish to assess data quality.
3. Format Conversion: Preparing sequences for the assembly engine.
4. Assembly: Executing hifiasm for high-fidelity contig generation.

K-mer Analysis Insights

The k-mer analysis is a crucial step in plant genomics. It allows us to:

• Predict the genome size.
• Identify the level of duplication and repeats.
• Optimize assembly parameters.

Analogy: If assembly is building a house, K-mer analysis is checking the quality and quantity of bricks before the first wall is even raised.

How to Run

bash

Clone the repository

git clone https://github.com/daniil-11-ger/oryza-sativa-genome-assembly.git

Run the pipeline

bash scripts/assembly_pipeline.sh

Pipeline Stages

Scaffolding (RagTag): Organized contigs into chromosomes using a reference-guided approach (IRGSP-1.0).

Organelle Sorting: Identified and separated chloroplast and mitochondrial genomes (nc_001320.1 and nc_011033.1).

Gene Prediction (Augustus): Performed ab initio gene prediction with extrinsic hints specifically for Oryza sativa.

Website

https://daniil-11-ger.github.io/oryza-sativa-genome-assembly/

Future Directions

• Repeat Masking: Refine the EDTA/RepeatMasker stage for better soft-masking before annotation.
• Functional Annotation: Using BLAST/InterProScan to assign biological functions to the predicted genes.
• Synteny Analysis: Comparing the Kasalath assembly with other rice cultivars.