What is the PeakTrace Basecaller
PeakTrace is a sanger DNA sequencing basecaller and trace processor that provides better basecalling and improves the appearance and read length of DNA sequencing traces by up to 50%.
The PeakTrace Basecaller works with all ABI sequencers including the ABI 377, ABI 310, ABI 3700, ABI 3730, ABI 3730xl, ABI 3100, ABI 3500, and ABI 3130.
Figure 1. Compared of KB and PeakTrace (PT) basecaller. This example shows the same trace file but just processed with the two different basecallers.
The real improvement in sequence quality provided by PeakTrace is shown in Figures 2 and 3. These show the alignment of the sequence data from the Figure 1 trace file BLAST aligned to the true sequence. The alignable sequence is not only much longer with PeakTrace than KB (1540 bases verse 1379 bases), but the first error is at nucleotide 1084 for KB and 1251 for PeakTrace.
Figure 2. BLAST alignment of KB basecalled trace against the true sequence. The 1% error read length is 1275 bases.
Figure 3. BLAST alignment of the PeakTrace basecalled trace against the true sequence. The 1% error read length is 1486 bases.
Common questions asked about PeakTrace
How is PeakTrace different to other basecaller like ABI’s KB Basecaller or phred?
Put simply, PeakTrace is just a better basecaller than KB in exactly the same way that KB is a better basecaller than phred or the old ABI basecaller. KB was a breakthrough basecaller when released more than 12 years ago and PeakTrace is just a further improvement in basecalling technology over KB. PeakTrace provides longer reads, more high quality bases, and better looking traces than KB or any other DNA basecaller.
Can I trust the sequence data from PeakTrace?
Nucleics has extensively validated PeakTrace to ensure that basecall quality assignment is accurate. The process of validating a basecaller is not simple or easy, but if you trust the KB Basecaller then you can trust PeakTrace.
How can I use PeakTrace?
There are four ways to use PeakTrace. The easiest is to just use the free online version of PeakTrace. This version is designed for users who only a need to basecall a few traces, or who want to see what PeakTrace can offer on their own data. It provides exactly the same quality as the paid versions, however, it is limited in the setting that can be used and you are limited to processing six traces per day.
The second way is to use Chromos 2.60 (or higher). This version of the free Chromas trace viewer incorporates the PeakTrace Basecaller. First time users of Chromas receive 20 free PeakTrace processing units and additional units can be purchased as needed from our online store.
If you want to basecall more traces you need to register to use Auto PeakTrace RP. After registering you will need to purchase a number of PeakTrace basecalling units from our online store (you can pay by credit card or Paypal). Once you have purchased a number of units you will then be provided with the password to download the Auto PeakTrace RP software from the Nucleics Download page.
The final way is to use PeakTrace is via our standalone PeakTrace:Box system. This is a complete hardware/software system that you can install at your facility and run PeakTrace locally without the need to upload your traces to our server. The PeakTrace:Box system is ideal for users who need to basecall a large numbers of traces, or for customers with strict privacy needs. For more information on the PeakTrace:Box system please visit the PeakTrace:Box overview page.
How much does Auto PeakTrace RP cost?
The Auto PeakTrace RP software is free, but to use it you must register to obtain a copy of the software. Once registered, you will need to purchase some processing units from our online store, or establish a standing account with us. Auto PeakTrace RP provides full user control over all the trace processing and basecalling parameters. These units can also be used with Chromas version of PeakTrace. The current prices to purchase Auto PeakTrace RP basecalling units are:
|100 PeakTrace Basecallings||US$30.00|
|1000 PeakTrace Basecallings||US$225.00|
|2000 PeakTrace Basecallings||US$400.00|
|10 000 PeakTrace Basecallings||US$1100.00|
|25 000 PeakTrace Basecallings||US$2000.00|
How much does the PeakTrace:Box system cost?
The monthly lease prices for the PeakTrace:Box systems 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 system (up to 500, 1000, 2000 traces per month) 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 PeakTrace and return the hardware. Importantly, we offer additional discounts on the PeakTrace:Box system for long term contracts and/or higher volumes.
Am I charged for traces not improved by PeakTrace?
No. Except in a couple of unusual circumstances if your sequence traces are not improved by the PeakTrace basecaller then you are not charged for the processing. This means you can use PeakTrace with confidence and not worry about paying for failed reactions – wouldn’t it be nice if BigDye™ came with the same guarantee!
Which version of PeakTrace should I use?
Can I try PeakTrace for free?
What setting are used with the free version of PeakTrace?
How do I purchase PeakTrace?
If I purchase PeakTrace will you keep my traces?
The bottom line is we never examine the data of our customers without their permission.
How does PeakTrace work?
PeakTrace is the result of more than 17 years of R&D at Nucleics focused on improving DNA sequencing. While developing products like the CounterTrace DNA sequencing system, CounterTrace II DNA sequencing system and LongTrace we learnt a great deal about how to best process and basecall the raw data of DNA sequencing traces. The algorithms that we developed for theses past products is what allows the PeakTrace basecalling software to extract more usable and accurate bases from each trace. For more information about what PeakTrace can do and how it can be used please visit the PeakTrace Basecaller overview page.
I want to know more about PeakTrace
We have release a whitepaper on PeakTrace on the validation of both the PeakTrace and KB basecallers. Please download the PeakTrace Whitepaper to learn more or visit the PeakTrace FAQ page. If you are interested in the basecaller validation process we have provided the validation process we performed for PeakTrace.