ARAMIS

ARAMIS corrects insertions and deletions (indels) in long-read genome assemblies by integrating PacBio long-read data with high-accuracy Illumina short reads to improve assembled-genome accuracy.

Key Features:

• Integrated Correction Pipeline: Combines multiple correction algorithms and leverages Illumina short-read data to correct indel errors in PacBio long reads.
• Efficiency and Resource Optimization: Provides superior correction with reduced computational demands compared to existing approaches.
• Error Characterization: Analyzes the nature and genomic distribution of indel errors, including systematic biases affecting homopolymeric regions.
• Adaptability to Diverse Genomes: Applied to six organisms with varying GC content, genome size, and genomic complexity.

Scientific Applications:

• Comparative Genomics: Produces accurate assemblies that facilitate comparative analyses across species or strains.
• Functional Genomics: Ensures functional annotations are based on corrected sequences free of indel-induced artifacts.
• Evolutionary Studies: Enables investigation of evolutionary processes and genetic diversity using high-fidelity long-read assemblies.

Methodology:

Combine PacBio long reads with high-accuracy Illumina short reads; apply a suite of correction algorithms to identify and correct indels; perform systematic error analysis to detect patterns related to GC content and homopolymeric regions.