sangerseqR

sangerseqR performs parsing, basecalling, chromatogram visualization, and deconvolution of mixed Sanger sequencing chromatogram data (.scf, .ab1) to identify heterozygous indels and characterize mutations in genome editing and related analyses.

Key Features:

• File compatibility: Reads and processes Sanger chromatogram file formats .scf and .ab1.
• Basecalling: Converts raw chromatogram signal into nucleotide sequence calls.
• Chromatogram plotting: Generates chromatogram plots for visual inspection of trace peaks and base calls.
• Mixed-peak (double peak) handling: Detects and addresses double peaks arising from heterozygous regions or indels in chromatograms.
• Allele separation: Implements an algorithm inspired by Poly Peak Parser to separate ambiguous base calls into distinct wild-type and mutant allele sequences.
• Indel characterization: Supports identification and characterization of insertions and deletions directly from single-run PCR-derived chromatograms.

Scientific Applications:

• Genome editing screening: Identification of indels and mutation sequences in samples following ZFN, TALEN, and CRISPR editing.
• F1 mutation genotyping: Detection and characterization of heterozygous indels in F1 individuals.
• Single-run PCR product analysis: Characterization of mutations from single PCR amplicon sequencing runs spanning targeted sites.
• General heterozygous indel detection: Application to contexts requiring identification of mixed alleles and indels from Sanger traces.

Methodology:

Parses .scf and .ab1 chromatogram files, performs basecalling and chromatogram plotting, and applies a Poly Peak Parser–inspired algorithm to deconvolute mixed ("double peak") chromatograms into separate wild-type and mutant allele sequences for indel detection.