PeakTrace:Box Basecaller System



PeakTrace:Box™ is a new DNA basecalling system for improving the read length of sequencing traces collected on the ABI 377, 310, 3730 3730xl, 3700, 3100, 3130, 3500 and MegaBACE DNA sequencers. The PeakTrace:Box system offers the following features:

  • Up to 50% more Q20+ bases per trace.
  • Compatible with traces obtained from all ABI DNA sequencers.
  • Compatible with traces obtained from MegaBACE DNA sequencer
  • An all-in-one system with an easy to use graphical user interface (Auto PeakTrace) that makes it simple to integrate PeakTrace into existing sequencing workflows and LIMS systems.

PeakTrace:Box DNA sequencing system

Current state of the art capillary DNA sequencers, such as the ABI 3500 series, generate reads that can easily exceed 1000 bases. Unfortunately,  reads often display low quality and high base call error rates in the later part of the trace (i.e. past base 850).


Figure 1. Example of the difference between the ABI KB basecaller and PeakTrace basecaller on the same trace file. This example is taken from an ABI 3130 trace from base position 1130 to 1180.

PeakTrace uses a novel approach to extract more high quality basecalls from the poorly resolved end regions. The PeakTrace software reprocesses the raw data contained within each ABI trace file using a series of highly sophisticated algorithms developed by Nucleics before being basecalled. This provides significantly better base and quality calls. An comparison of PeakTrace basecalling with the ABI KB basecaller is shown in Figure 1.

The PeakTrace:Box is a complete system where all trace basecalling can be performed within the facility. This alleviates possible privacy concerns users may have with our server based Auto PeakTrace RP basecaller. The system comes with an easy to use graphical software (Auto PeakTrace) which allows sequencing facility staff automate the PeakTrace basecalling process in a simple and reliable manner.

Features & Benefits of the PeakTrace:Box System

Simple to use

The PeakTrace:Box DNA sequencing system is simple to both set up and use. The system uses a secure USB Key to provide off-line licensing. The USB key can be used with any computer supporting SSE3 (Intel Core processor or better).


The PeakTrace:Box also comes with a Windows graphical administration software (Auto PeakTrace™) that allows DNA sequencing facility managers to automate the PeakTrace basecalling of ABI files located anywhere on the network. In addition, the Auto PeakTrace software provides a series of tab delimited processing reports (log files) for both the final end users and facility managers. The reports provide users with information on the basecalling improvements as well as why the trace was not able to be improved.

The PeakTrace:Box system is as available as an Linux X86_64 command line version that enables PeakTrace basecalling to be simply integrated in Linux based LIMS workflows.

Increases trace read length and reduces errors

PeakTrace provides the user with significantly longer and higher quality reads. These improved read lengths mean that fewer sequencing reactions need be performed to complete a sequencing project, thus saving the investigator significant time and money. In addition, as the PeakTrace basecaller is compatible with older DNA sequencer like the ABI 377 and 3700 it is able to extend the effective life of these instruments by offering traces read length comparable with that obtained from modern instruments such as the ABI 3500 or 3730.

The improved read lengths provided by PeakTrace:Box increase sequence throughput and significant lower the overall per base cost. In addition, these longer read lengths enable sequencing projects (e.g. whole-genome, cDNA clones, etc) to be completed at lower sequence coverage levels, thus offering further cost and time savings.

The PeakTrace:Box system is available at six standard throughput levels (500, 1000, 2000, 5000, 10,000 or 25,000 processing per month) plus large custom scales with pricing ranging from 4 cents per trace. The standard monthly prices are

500 traces per month systemUS$150.00
1000 traces per month systemUS$225.00
2000 traces per month systemUS$400.00
5000 traces per month systemUS$800.00
10 000 traces per month systemUS$1100.00
25 000 traces per month systemUS$2000.00

The three PeakTrace:Mini system (500, 1000, 2000) have an additional once-only hardware set-up fee of US$200. For leases of less than six month we may require a deposit on the hardware which is refund if you choose to stop using Auto PeakTrace and return the hardware. We offer additional discounts on the PeakTrace:Box system for long term contracts and/or higher volumes.

For further information on PeakTrace:Box please email us at {This email is obscured. Your must have javascript enabled to see it} with your questions or visit our PeakTrace:Box Forum.