Introduction
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 and MegaBACE DNA sequencers. The PeakTrace:Box offers the following features:
- Up to 100% more Q20+ bases per trace.
- Compatible with traces obtained from all ABI sequencers.
- Compatible with traces obtained from MegaBACE instruments.
- An all-in-one system with an easy to use graphical user interface (Auto PeakTrace) that makes it simple to integrate 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, 3100 or 3130 series, generate reads that can easily exceed 1000 bases. Unfortunately, the reads often display low quality and high base call error rates in the later part of the trace (ie post 850 bases).
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 re-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 ftp based PeakTrace basecalling service. 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 is based around a custom Apple Intel Mac Mini running Windows XP Professional. This allows the system to be accessed using the standard Windows file share network.
The PeakTrace:Box also comes with a graphical administration software (Auto PeakTrace™) that allows sequencing facility manager 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 for both the final end users and facility managers. The reports provide users with information on basecalling improvements as well as why the trace was not able to be improved.
Increases trace read length and reduces errors
PeakTrace provides the user with significantly longer and higher quality reads (Figures 1 & 2). 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 comparible with that obtained from modern instruments such as the ABI 3130 or 3730.
Figure 2. Example of PeakTrace basecalling on an ABI 377 trace file. The original ABI basecall is shown on top.
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 throughput levels (500, 1000, 2000, 5000, 10,000 or 25,000 processing per month) with pricing ranging from 6.4 to 18 cents per trace.
For further information on PeakTrace:Box please with our questions or visit our PeakTrace forum.