Compare Genome Assemblies

The Compare Genome Assemblies module enables users to compare key statistics across different genome assemblies. It is an essential tool for researchers and scientists who want to evaluate and contrast different assemblies of the same or related species. Below is an overview of the main features and metrics that can be compared using this module.

Key Features

• Multiple Genome Assemblies: Users can select multiple genome assemblies for comparison. The module provides a user-friendly interface where assemblies can be added or removed easily.

• Custom Metric Selection: Users can choose the metric they want to compare across the selected genome assemblies. This allows for flexible and targeted analysis of genome quality and characteristics.

• Visual Comparison: The module generates bar charts that provide a clear and visual representation of the chosen metric for each genome assembly. This helps users quickly identify differences and trends among the assemblies.

Available Metrics for Comparison

The module supports the comparison of the following metrics across different genome assemblies:

1. GC Percentage

• The percentage of the genome that is composed of guanine (G) and cytosine (C) nucleotides. This can give insights into the genome's stability and structure.

2. Total Sequence Length

• The total length of the assembled genome, measured in base pairs. It reflects the overall size of the genome assembly.

3. Genome Coverage

• Indicates the average number of times a nucleotide in the genome has been sequenced. Higher coverage means more accurate and complete assemblies.

4. Scaffold N50

• The length of the shortest scaffold such that 50% of the total assembly length is in scaffolds of this length or longer. A higher scaffold N50 value indicates a more contiguous assembly.

5. Contig N50

• The length of the shortest contig such that 50% of the total assembly length is in contigs of this length or longer. Similar to scaffold N50 but focusing on contigs, it reflects the quality of the assembly at the contig level.

6. PN50 Ratio

• The PN50 ratio is a metric for pseudochromosome assemblies. It compares scaffold lengths and is particularly useful in assemblies that aim to represent the genome at a chromosome level.

Example Comparison

In the provided image, the selected metric for comparison is the PN50 ratio. The bar chart shows the PN50 ratio for four genome assemblies:

• USDA_CsJoelle
• ASM3068613v1
• CO46V2.0
• Cs

This visual comparison helps users quickly assess which assemblies have higher or lower PN50 ratios, providing insight into the quality and contiguity of the genome assemblies at the chromosome level.

How to Use

1. Select Genome Assemblies: Use the dropdown menu to choose the genome assemblies you want to compare.

2. Choose a Metric: Select the metric you wish to compare from the available options: GC Percentage, Total Sequence Length, Genome Coverage, Scaffold N50, Contig N50, or PN50 Ratio.

3. View Results: The module generates a bar chart that visually represents the chosen metric for each genome assembly, enabling a quick comparison.

Importance for Researchers

This module is highly beneficial for plant breeders, bioinformaticians, and researchers working on genomic studies, especially for species such as Camelina sativa. The ability to compare multiple assemblies across a variety of metrics helps users choose the best assembly for downstream analysis. It also provides insights into the assembly process, allowing for improvements in future assembly efforts.

The visual format of the comparisons ensures that data can be easily interpreted and acted upon, making the Compare Genome Assemblies module a vital tool for comparative genomics.