PeakTrace:Box

PeakTrace:Box is a standalone DNA basecalling system developed by Nucleics for improving the read length and quality of sequencing traces generated on ABI DNA sequencers, including the 377, 310, 3700, 3100, 3130, 3200, 3500, 3600, 3730, and 3730xl models. It is designed for use within sequencing facilities that require on-site basecalling, avoiding the need to send trace data to an external server.

The system reprocesses raw data contained within ABI .ab1 trace files using proprietary algorithms developed by Nucleics scientists. This approach targets the poorly resolved end regions of traces — typically past base 850 — where standard basecallers such as the ABI KB Basecaller produce high error rates and low-quality calls. PeakTrace:Box performs all basecalling locally within the facility, addressing data privacy concerns associated with server-based alternatives.

Key Features and Benefits

• Delivers up to 50% more high-quality bases per trace compared to standard basecallers.
• Increases sample throughput by up to 300% more samples per day.
• Rescues low-quality and failed reads, reducing the need for repeat sequencing reactions.
• Compatible with traces from all ABI DNA sequencer models.
• Extends the effective working life of older instruments such as the ABI 377 and 3700 by producing read lengths comparable to modern instruments like the ABI 3500 or 3730.
• Reduces noise and improves peak resolution in .ab1 trace files, aiding detection of polymorphic sites and mixed basecalls.
• Longer read lengths allow sequencing projects — including whole-genome and cDNA clone projects — to be completed at lower coverage levels, reducing per-base cost and time.

Software and Workflow Integration

• Includes Auto PeakTrace, a Windows graphical user interface that allows facility managers to automate PeakTrace basecalling of ABI files located anywhere on the network.
• Auto PeakTrace generates tab-delimited processing reports (log files) for end users and facility managers, covering basecalling improvements and reasons why a trace could not be improved.
• Auto PeakTrace can be called from the command line, enabling integration into existing data processing scripts and LIMS workflows.
• Also available as a Linux x86_64 command-line version for integration into Linux-based LIMS environments.
• Uses a secure USB key for offline licensing.

Pricing and Licensing

• Pricing is based on actual basecalling volume, with sliding discounts for larger volumes and longer lease periods.
• Per-trace costs can be as low as US$0.02 per .ab1 file depending on volume, lease period, and settings used.
• PeakTrace:Mini systems (under 100,000 units per year) carry a one-time hardware setup fee of US$500.
• Leases of less than six months may require a refundable deposit of US$300 per USB key.
• Includes a 60-day full money-back guarantee; the system can be returned within 60 days for a full refund.

Pricing quotes can be requested by contacting Nucleics at [email protected]. A free trial of the PeakTrace basecaller on user-supplied traces is available via the PeakTrace Online service.