PeakTrace Basecaller

PeakTrace Basecaller, developed by Nucleics, is a DNA sequencing basecalling software designed to extract longer, higher-quality sequence reads from trace files collected on Applied Biosystems (ABI) DNA sequencers. It is intended for use in core sequencing laboratories, genome sequencing projects, and any setting where maximising read length and reducing per-base sequencing costs are priorities. The software is compatible with the ABI 377, 310, 3700, 3730, 3730xl, 3100, 3130, 3200 (SeqStudio), 3500, and 3600 (SeqStudio Flex) instruments.

Automated DNA sequencers can collect reads exceeding 1400 nucleotides, but the region beyond base 850 typically contains broad, overlapping peaks associated with low quality scores and high error rates. PeakTrace addresses this by applying a proprietary series of algorithms to reprocess the raw data within each .ab1 trace file, enabling more accurate base and quality calls in these poorly resolved regions and improving the visual appearance of the peaks.

Key Capabilities

• Extracts up to 50% more high-quality bases per trace compared to standard basecalling.
• Supports up to a 3x increase in effective DNA sequencer throughput.
• Improves detection of polymorphic bases.
• Reduces the number of traces falling below 100 bases, improving overall trace pass rates.
• Produces standard .ab1 output files, maintaining compatibility with downstream applications such as Staden and Phrap.
• Compatible with all ABI DNA sequencing instruments, including normal and rapid run traces collected at high run voltages above 12 kV.
• Can be applied retrospectively to previously collected trace data, allowing reassembly of existing sequencing projects without collecting new data.

Available Versions

• Auto PeakTrace RP — a server-based version where trace files are uploaded to the PeakTrace server for processing and downloaded to the user's selected output folder upon completion. Users purchase processing units and install the client software on their own computer. Available for Windows (XP, Vista, Win7, Win8, Win10).
• PeakTrace:Box — a fully offline version supplied with a USB key for licensing. Available as either a graphical interface (Auto PeakTrace) or a command-line version (peaktrace) to support automated processing and integration with existing LIMS. Provides log reports suitable for core lab environments where users are charged on a per-trace basis. Available for Windows (XP, Vista, Win7, Win8, Win10) and x86_64 Linux.

Trial and Evaluation

• A free PeakTrace Online basecalling service is available, providing the same basecalling quality as the paid versions but limited to 250 traces per day.
• The online trial allows users to evaluate the basecaller on their own trace files before purchasing.
• For larger volumes, Nucleics recommends purchasing an Auto PeakTrace RP account.

Workflow — Auto PeakTrace RP

1. Open an Auto PeakTrace RP account and purchase processing units.
2. Download and install the RP client software on a local computer.
3. Select the input folder containing .ab1 trace files and configure basecalling settings via the options window.
4. Traces are automatically uploaded to the PeakTrace server for processing.
5. Basecalled traces are downloaded by the RP software to the selected output folder on the user's computer.

PeakTrace:Box supports integration into existing laboratory information management systems via its command-line interface and is suitable for both individual researchers and core sequencing facilities. Further information, including purchasing options and a downloadable whitepaper, is available from Nucleics at [email protected].