PeakTrace:Box Basecaller System

PeakTrace:Box™ is a novel DNA basecalling system for improving the read length of sequencing traces collected on the ABI 377, 310, 3730 3730xl, 3700, 3100, 3130, 3200, 3500, 3600 DNA sequencers. The PeakTrace:Box system offers the following features

• Up to 50% more high quality bases per trace.
• Improved appearance of traces that result in increased customers.
• Rescue of low quality and failed reads saving money.
• Increased throughput – up to 300% more samples per day.
• Compatible with traces obtained from all ABI DNA sequencers.
• An all-in-one system with an easy to use graphical user interface (Auto PeakTrace) that makes it simple to integrate PeakTrace Basecalling into existing sequencing workflows and LIMS systems.

PeakTrace:Box DNA Sequencing System

Current state of the art capillary DNA sequencers, such as the ABI 3730 & 3600 series, generate reads that can easily exceed 1000 bases. Unfortunately, the traces often display low quality and high basecall 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 3730 trace from base position 1030 to 1070.

PeakTrace uses a novel data processing 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 and proprietary algorithms developed by Nucleics’s scientists before being re-basecalled. This provides significantly better base and quality calls. A comparison of the PeakTrace Basecaller with the ABI KB Basecaller™ is shown in Figure 1 above.

PeakTrace:Box is a complete system where all trace basecalling is performed within the facility. This alleviates any 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 to automate the PeakTrace basecalling process in a simple and reliable manner. Auto PeakTrace can also be called from the command line enabling it to be easily integrated into existing data processing scripts.

Features & Benefits of the PeakTrace:Box System

Simple to use

The PeakTrace:Box DNA sequencing system is both simple to set up and use. The system uses a secure USB Key to provide offline licensing.

The PeakTrace:Box system comes with a Windows graphics 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 also available as a linux X86_64 command line version that enables PeakTrace Basecalling to be easily integrated in Linux-based LIMS workflows and scripts.

Increases trace read length and reduces errors

PeakTrace provides 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 time and money. In addition, as the PeakTrace Basecaller is compatible with older DNA sequencers like the ABI 377 and 3700, it is able to extend the effective life of these instruments by offering trace read lengths 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 significantly lower the overall per base cost. 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.

Improved trace appearance

PeakTrace improves the appearance of .ab1 trace files, reducing noise and hard to resolve peaks. This improved appearance helps the detection of polymorphic sites and mixed basecalls.

Pricing

The PeakTrace:Box system is priced on your actual basecalling needs with a sliding discount for large volumes and longer lease periods. While the exact cost per trace will depend on your actual volume, lease period, the settings used, and samples prices per trace can be as low as US$0.02 per .ab1. Please contact us {This email is obscured. Your must have javascript enabled to see it} for a pricing quote.

The PeakTrace:Mini systems (under 100 000 units per year) have an additional once only hardware set-up fee of US$500. For leases of less than six months we may require a deposit of US$300 per USB key, which is refunded if you choose to stop using PeakTrace and return the key.

PeakTrace comes with a 60 day, full money back guarantee. If you find that the PeakTrace:Box system does not meet your expectations for any reason you can return it within 60 days for a full refund – all we ask is that you tell us why you chose to cancel.

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. To try the PeakTrace basecaller for free on your own traces then please visit our PeakTrace Online page.