PacRAT

PacRAT improves the accuracy of barcode-variant mapping from PacBio long-read sequencing data by refining read alignment and consensus calling to reduce errors from sequencing artifacts.

Key Features:

• Barcode-variant mapping accuracy: Improves pairing of barcodes with genetic variants in barcoded genetic variant libraries.
• Read alignment refinement: Performs multiple steps of read alignment to refine mapping of long reads.
• Consensus calling: Applies consensus calling to reduce sequencing errors in aligned reads.
• PacBio long-read support: Operates on PacBio long-read sequencing data.
• Sequencing artifact error reduction: Reduces errors arising from sequencing artifacts.
• Validation by simulation: Demonstrated improved precision using simulations on eight variant libraries of varying lengths.

Scientific Applications:

• Barcode-variant association: Assigns barcodes to genetic variants in barcoded variant libraries for downstream genotype-phenotype analyses.
• Analysis of diverse libraries: Evaluates barcode-variant associations across variant libraries of varying lengths and compositions.
• Error correction in PacBio datasets: Mitigates sequencing-artifact errors in analyses of PacBio long-read sequencing data.

Methodology:

Performs multiple steps of read alignment and consensus calling to refine barcode-variant mapping; evaluated by simulations using eight variant libraries of varying lengths.