Gear-Genomics

Gear-Genomics analyzes Sanger sequencing chromatograms, designs PCR primers, and performs DNA sequence analyses to support variant validation and genome editing confirmation.

Key Features:

• Tracy command-line application: A command-line tool for Sanger sequencing data analysis providing basecalling, alignment, assembly, and deconvolution of chromatogram files.
• Sanger chromatogram analysis: Processing and interpretation of Sanger sequencing traces and chromatogram files for variant detection and sequence validation.
• PCR primer design: PCR primer design capabilities for targeted amplification and validation experiments.
• Pipeline and high-throughput integration: Command-line integration suitable for incorporation into large-scale pipelines and high-throughput workflows.
• Structured output formats: Reporting of sequencing results and variant calls using JSON and BCF file formats.

Scientific Applications:

• Clinical genomics validation: Support for large-scale validation efforts in clinical genomics through Sanger-based confirmation of variants.
• Genome editing confirmation: Rapid confirmation of discovered variants or engineered mutations in genome editing workflows.
• Molecular biology sequence analyses: Detailed DNA sequence analyses for molecular biology investigations relying on Sanger data.

Methodology:

Basecalling, alignment, assembly, and deconvolution of Sanger chromatogram files using the Tracy command-line application with results exported in JSON and BCF for pipeline integration.