A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector.

Area of Science:

• Genomics
• Bioinformatics

Background:

• Long-read sequencing generates extensive DNA sequences, crucial for assembling complex and repetitive genomic regions.
• Despite advancements, genome assembly errors persist due to genomic complexity and technological limitations, necessitating robust evaluation methods.

Purpose of the Study:

• To introduce Inspector, a versatile tool for evaluating long-read genome assemblies.
• To highlight Inspector's capabilities in reference-free and reference-guided evaluation, error detection, and correction.

Main Methods:

• Demonstration of four distinct procedures using Inspector for long-read assembly evaluation.
• Utilizing Inspector's features for detecting small and large structural errors and performing haplotype-resolved analysis.

Main Results:

• Inspector offers comprehensive assembly evaluation beyond basic statistics.
• The tool precisely locates and categorizes various structural errors within genome assemblies.
• Inspector's error correction feature enhances the quality of existing assemblies.

Conclusions:

• Inspector provides a robust framework for evaluating long-read genome assemblies.
• Its advanced features, including error correction and haplotype resolution, significantly improve assembly quality assessment.