Developer: Merck Sharp & Dohme LLC (Merck & Co., Inc.) & UCT Prague
Supported platforms: Web browser / Self-hosted Docker, Linux, macOS, Windows (Python / Flask + Celery + Redis)
Download / Source: https://github.com/MSDLLCpapers/TraceTrack
Features
View Quality scores
Yes. Uses embedded base quality scores for threshold filtering and quality-based end trimming across batches.
View raw data
Displays aligned four-colour trace electropherograms beneath consensus and amino-acid translations rather than unprocessed capillary voltage traces.
Assembly
Yes. Batch-aligns hundreds of Sanger reads against user-supplied reference sequences using Clustal Omega (automatically detects reference IDs in filenames or chooses the highest-scoring forward/reverse orientation), highlights discrepancies, and classifies variants.
Input file formats
.ab1 trace files or .zip archives of .ab1 files (note: .scf is not supported), plus reference sequences in FASTA, GenBank (.gb), .csv, or .xlsx.
Output file formats
Interactive multi-sheet Excel (.xlsx) reports with hyperlinked alignment summaries, consensus sequences, amino-acid translations, and mismatch/zero-coverage tables.
Trimming
Yes. Automated threshold-based quality end-trimming (requires three consecutive bases above the quality threshold; manual trimming is not supported).
Integrated Blast
No.
Open multiple windows
Yes, via browser tabs and multi-trace aligned chromatogram inspection panels.
Edit bases
No—base calls are intentionally immutable for reproducible QC reporting.
ABI limits (regions outside of clear range region are displayed in gray)
No (uses configurable quality-threshold end trimming).
Other functions
- Secondary-peak detection uses a default
0.15fraction in the implementation to highlight double peaks in high signal-to-noise regions - Continuous CDS translation classifying silent, missense, nonsense, and frameshift mutations
- Click-to-jump mutation navigation bar and self-hosted Docker deployment for confidential pharma/biotech sequences
Cost
Free and open source (GPL-3.0).
Comments
TraceTrack was engineered by Merck researchers specifically for high-throughput screening of plasmid libraries, antibody cloning, and protein-engineering plates. Because you can deploy it locally via Docker, biotech teams get reproducible batch alignment, secondary-peak alerts, and Excel deliverables without sending sequences off-premises (just remember it requires .ab1 rather than .scf files).
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.