Genome Continuity Inspector (GCI)

Genome Continuity Inspector (GCI) assesses genome assembly continuity at single-base resolution to evaluate telomere-to-telomere (T2T) genome assemblies.

Key Features:

• Single-base resolution assessment: GCI evaluates genome assembly continuity at single nucleotide resolution to reflect true completeness and distinguish nearly T2T from truly T2T assemblies.
• Long-read mapping: GCI utilizes multiple aligners to map long reads from multiple sequencing platforms back to the assembly.
• Curated coverage analysis: GCI incorporates curated mapping coverage of high-confidence read alignments to identify potential assembly issues.
• GCI scoring: GCI reports scores to quantify assembly overall continuity at whole genome or chromosome scale.

Scientific Applications:

• T2T assembly qualification: GCI provides a universal standard to qualify whether a genome assembly meets T2T level by evaluating true continuity rather than relying on metrics like N50 that are independent of raw reads and can be inflated by artificial operations.
• Assembly issue identification: GCI identifies and quantifies potential assembly issues through coverage-based analysis of long-read alignments.

Methodology:

GCI maps long reads from multiple platforms to the assembly using multiple aligners, then incorporates curated mapping coverage of high-confidence read alignments to identify assembly issues and calculate continuity scores.