ICORN

ICORN iteratively corrects reference genome nucleotides by aligning deep-coverage short sequencing reads to identify and fix discrepancies in the reference sequence.

Key Features:

• Iterative Alignment: Employs iterative alignment of sequencing reads against the reference to detect and correct nucleotide discrepancies.
• Deep Coverage Utilization: Utilizes deep coverage of short sequencing reads to detect rare errors with high confidence.
• High Accuracy: Demonstrated on the Plasmodium falciparum genome (81% A+T), identifying and correcting over 2000 reference errors.
• Broad Applicability: Applicable to a variety of eukaryotic and prokaryotic genomes.

Scientific Applications:

• Evolutionary Biology: Provides more accurate reference sequences for evolutionary analyses and phylogenetic studies.
• Comparative Genomics: Improves sequence fidelity for cross-species genome comparisons.
• Functional Genomics: Enhances gene annotation and interpretation of functional elements by reducing reference errors.
• Variant Calling: Reduces false positives and false negatives in variant detection by correcting reference inaccuracies.
• Large-Scale Genomic Projects: Supports automated correction workflows for large-scale sequencing projects without manual intervention.

Methodology:

ICORN performs iterative alignment of short sequencing reads to the reference, incorporates corrections from each cycle into the reference, and repeats iterations until convergence is achieved.