From Short Reads to Chromosome-Scale Genome Assemblies

Area of Science:

• Genomics
• Bioinformatics
• Oomycete and Fungal Research

Background:

• High-quality genome assemblies are crucial for downstream biological studies.
• Current commercial software may lack the flexibility for nonmodel organisms like oomycetes and fungi.
• Customizing assembly workflows is essential for optimizing results for specific species.

Purpose of the Study:

• To present a modular workflow for de novo genome assembly and annotation.
• To guide researchers in selecting and applying appropriate tools for each assembly step.
• To enable the generation of high-quality, chromosome-scale, or draft genome assemblies.

Main Methods:

• Raw read processing and quality control.
• Initial genome assembly generation using selected software.
• Iterative optimization, scaffolding, and chromosome-level assembly.
• Annotation of the final genome assembly.

Main Results:

• A comprehensive, modular workflow for genome assembly and annotation is detailed.
• Examples and alternative software options are provided for each step.
• The workflow is adaptable for various organisms, including pathogenic oomycetes and fungi.

Conclusions:

• Researchers can customize genome assembly workflows using appropriate tools for their specific organism.
• This approach facilitates the creation of high-quality, annotated genome assemblies for diverse research needs.
• The presented workflow supports both validated chromosome-scale assemblies and high-quality draft assemblies.