Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Illumina sequencing technology has made yeast genome sequencing accessible and affordable.
• While genome assembly is routine, interpreting the contents of these assemblies remains a challenge.
• The SPAdes assembler is widely used for *de novo* yeast genome assembly.

Purpose of the Study:

• To develop a method for investigating the nature and quality of yeast genome assemblies.
• To identify and diagnose potential problems within genome assemblies generated by SPAdes.
• To provide tools for filtering contaminants and understanding complex assembly structures.

Main Methods:

• Utilizing Coverage-vs.-Length (CVL) plots to visualize scaffold length and coverage data from SPAdes assemblies.
• Identifying high-coverage scaffolds indicative of mitochondrial DNA, ribosomal DNA, and plasmids.
• Detecting low-coverage contaminants, including cross-contamination and molecular standards (PhiX174, Lambda DNA).
• Analyzing scaffold patterns in heterozygous genomes to distinguish separate alleles from collapsed co-assemblies.

Main Results:

• CVL plots effectively differentiate between various types of genomic elements and contaminants based on coverage.
• High coverage identifies organellar DNA and plasmids, while low coverage flags contaminants.
• Heterozygous genomes show distinct scaffold patterns related to allele separation or collapse.
• A Python script is provided to filter assemblies based on CVL plot analysis.

Conclusions:

• CVL plotting is a simple yet powerful method for assessing yeast genome assembly quality and structure.
• This approach aids in identifying and removing contaminants, leading to more accurate genome representations.
• The visualization and filtering tools enhance the interpretation of complex yeast genomes, including hybrids.