PeakTrace Basecaller

What is the PeakTrace Basecaller

PeakTrace is a Sanger DNA sequencing basecaller and trace processor that provides better basecalling and improve 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. PeakTrace also supports the MegaBACE DNA sequencers.


Figure.1. PeakTrace compared to KB. This example shows the same sequencing trace at the same position but just processed with the two different basecallers.

Common questions asked about PeakTrace

How is PeakTrace different to other basecaller like ABI’s KB Basecaller?

Put simply, PeakTrace is 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 when released more than 10 years ago and PeakTrace is a further improvement over KB. PeakTrace provides longer reads, more high quality bases, and better looking traces than KB or any other DNA basecaller.

How can I use PeakTrace?

There are three ways to use PeakTrace. The easiest is to use the free online version of PeakTrace which is designed for users with only a need to basecall a few traces or want to see what PeakTrace can offer on their own data. This provides exactly the same quality as the paid services, however, you are limited to processing only 6 traces per day.main_window_rp_540

If you need to basecall more traces then 6 per day you will need to register for Auto PeakTrace RP. After registering you will purchase a number of PeakTrace basecalling units from our online store, or establish a standing account with us. You will then be provided with the password to download the Auto PeakTrace RP software from the Nucleics Download page.

The third way is to use PeakTrace is via our standalone PeakTrace Basecaller, the PeakTrace:Box system. This is a complete hardware/software system that you can install in your facility and run PeakTrace locally without the need to upload your traces to our server. The PeakTrace:Box system is ideal for users with large numbers of traces to process, or for customers with privacy concerns or needs. For more information on the PeakTrace:Box system please go to the PeakTrace:Box overview page.

To visually compare the read length improvements offered by PeakTrace we recommend you use a trace viewing application like the ABI Sequencing Analysis or Chromas.

How much does Auto PeakTrace RP cost?

The Auto PeakTrace RP software is free, but to use it you need to register to obtain a copy of the software. Once registered, you need purchase processing units from our online store or establish a standing account with us. Auto PeakTrace RP provides control over the trace processing and basecalling parameters. The current prices to purchase Auto PeakTrace RP basecalling units are:

100 PeakTrace BasecallingsUS$30.00
1000 PeakTrace BasecallingsUS$225.00
2000 PeakTrace BasecallingsUS$400.00
10 000 PeakTrace BasecallingsUS$1100.00
25 000 PeakTrace BasecallingsUS$2000.00

How much does the PeakTrace:Box system cost?

The monthly lease prices for the PeakTrace:Box systems 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 PeakTrace and return the hardware. Importantly, we offer additional discounts on the PeakTrace:Box system for long term contracts and/or higher volumes.

If you are processing more than 4000 traces per month then the box system is most likely to better suited for your needs, but we recommend that you discuss your requirements with us. If you are generating less than 2000 traces per month then the Auto PeakTrace RP is likely to be the best fit for your needs. If you are in any doubt as to which system will best fit your needs please contact us at {This email is obscured. Your must have javascript enabled to see it}.

Am I charged for traces not improved by PeakTrace?

No. Except in a couple of unusual circumstances if your sequence trace is not improved by the PeakTrace basecaller then you are not charged for it. This means you can use PeakTrace with confidence and not worry about paying for failed reactions – it would be nice if BigDye came with the same guarantee.

Which version of PeakTrace should I use?

This is a difficult question to answer as it depends on your particular needs and circumstances. Try the free online PeakTrace version to see what PeakTrace can do for your own traces and then contact our sales team at {This email is obscured. Your must have javascript enabled to see it} and we can advise you on the best version for your needs.

Can I try PeakTrace for free?

Yes. We offer a free web-based version of PeakTrace which you can try for free. You do not need to register to use this version. The basecalling from the free PeakTrace software is exactly the same as the Auto PeakTrace RP and PeakTrace:Box systems. The only limitation with the free version is that you are limited to processing less than 6 traces per day. If you need to process more than this many traces per day then please contact us at {This email is obscured. Your must have javascript enabled to see it}.

How do I purchase PeakTrace?

To buy PeakTrace basecalling units please visit our secure online shop. If you expect to be basecalling over 4000 traces per month please contact our sales team  at {This email is obscured. Your must have javascript enabled to see it} as we offer significant discounts for large standing orders.

To purchase the PeakTrace:Box system please contact our sales team at {This email is obscured. Your must have javascript enabled to see it} with your monthly sequencing volume and they will provide a quote.

If I purchase PeakTrace will you keep my traces?

No. We have a very strict privacy policy regarding your data (please see our privacy policy for more details). If you use the PeakTrace:Box system we never see your sequences. The Box system it can be run without an network connection is so desired.

The bottom line is we will never examine the data of our customers without their permission. 

How does PeakTrace work?

PeakTrace is the result of more than 16 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 the past products is what allows the PeakTrace basecalling software to extract more usable 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. Download the PeakTrace Whitepaper to learn more.

Please visit the PeakTrace FAQ page. If you have any further questions please contact our support team at {This email is obscured. Your must have javascript enabled to see it} or visit the PeakTrace forum to ask any question you may have.