sangeranalyseR

sangeranalyseR processes Sanger sequencing ABIF files to load and trim reads, detect secondary peaks, assemble and align contigs from multiple reads, detect insertions and deletions against a reference sequence, and visualize chromatograms for sequence analysis.

Key Features:

• Data Handling: Supports the ABIF file format to load and process Sanger sequencing data.
• Read Trimming and Secondary Peak Detection: Performs read trimming and detects secondary peaks in chromatogram traces.
• Contig Creation: Assembles contigs from collections of Sanger sequencing reads.
• Contig Alignment: Aligns assembled contigs for downstream sequence comparison and interpretation.
• Chromatogram Visualization: Provides chromatogram viewing for inspection of peak traces and base calls.
• Indel Detection: Detects insertions and deletions using a provided reference sequence.

Scientific Applications:

• NGS Validation: Validates variants and sequence calls from next-generation sequencing by confirming Sanger reads.
• Small-scale Sanger Projects: Processes and analyzes Sanger sequencing datasets for small laboratory-scale studies.
• Targeted Sequence Analysis: Performs targeted sequence analysis such as variant confirmation and amplicon characterization using Sanger data.

Methodology:

Computational steps explicitly include loading ABIF files, read trimming, detection of secondary peaks, assembly of contigs from multiple reads, alignment of contigs, indel detection against a reference sequence, and chromatogram visualization.