Hybrid-SHREC

Hybrid-SHREC performs error correction of mixed DNA sequencing reads from SOLEXA/Illumina, Roche/454, and Applied Biosystems SOLiD to improve read accuracy for de novo genome assembly.

Key Features:

• Platform Agnosticism: Handles mixed sequencing reads from SOLEXA/Illumina, Roche/454, and Applied Biosystems SOLiD.
• Color Space Read Correction: Corrects SOLiD color-space reads (two-base color coding) alongside base-space reads.
• High Sensitivity and Specificity: Achieves 99% sensitivity and >98% specificity when combined sequencing coverage is at least 12x.
• Reduction of Error Rates: Reduces overall substitution, insertion, and deletion error rates in sequencing reads.

Scientific Applications:

• De novo sequencing projects: Enables more accurate de novo genome assembly from mixed-platform datasets.
• Genome assembly and analysis: Improves the quality and reliability of genome assemblies and downstream analyses.
• Genomics, evolutionary biology, and personalized medicine: Supports research in these fields by improving read accuracy from diverse sequencing technologies.

Methodology:

An algorithm originally developed to correct base-space reads from SOLEXA/Illumina and Roche/454 was refined to accommodate SOLiD color-space reads.