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, 3500 and MegaBACE DNA sequencers. The PeakTrace:Box system offers the following features
- Up to 50% more Q20+ high quality bases per trace.
- Improved appearance of traces
- 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 & 3500 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 algorithms developed by Nucleics before being 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.
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.
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 USB key can be used with any computer supporting SSE3 (Intel Core processor or better).
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.
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.
The PeakTrace:Box system is available at six standard throughput levels (up to 500, 1000, 2000, 5000, 10,000 or 25,000 processing per month) plus larger scale pricing, ranging from 4 cents per trace. The standard monthly prices are
|Up to 500 traces per month system||US$150.00|
|Up to 1000 traces per month system||US$225.00|
|Up to 2000 traces per month system||US$400.00|
|Up to 5000 traces per month system||US$800.00|
|Up to 10 000 traces per month system||US$1100.00|
|Up to 25 000 traces per month system||US$2000.00|
The three PeakTrace:Mini systems (500, 1000, 2000) have an additional once-only hardware set-up fee of US$200. For PeakTrace leases of less than six months, we may require a deposit on the hardware which is refunded 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.