Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User...

Area of Science:

• Genomics
• Bioinformatics

Background:

• Sanger sequencing generates chromatogram files (e.g., .ab1) requiring manual processing for mutation detection.
• Analyzing both forward and reverse reads for a single sequence region is time-consuming, especially for large genes with multiple exons.

Purpose of the Study:

• To develop a rapid, automated command-line system for processing Sanger sequencing data.
• To streamline mutation detection workflows by automating sequence alignment and analysis.

Main Methods:

• The Automated Mutation Analysis Pipeline (ASAP) reads .ab1 files and converts them to FASTQ format.
• ASAP trims low-quality bases, reverse-complements reverse reads, and generates consensus sequences.
• The pipeline optionally extracts exonic regions, translates sequences, and performs nucleic acid and amino acid alignments.

Main Results:

• ASAP automates the filtering, building, and alignment of consensus sequences from raw Sanger data.
• The tool can extract exonic regions, translate them into all reading frames, and perform alignments.
• All generated files are suitable for further downstream analysis.

Conclusions:

• ASAP significantly reduces the time and effort required for analyzing Sanger sequencing data.
• This automated pipeline facilitates efficient mutation detection and genomic analysis.