What is the PeakTrace Basecaller
PeakTrace is a DNA sequencing basecaller that provides lower errors and improve the read length of ABI sequencing traces by up to 100%. The PeakTrace basecaller works with any trace produced by an ABI sequencer including the ABI 377, ABI 310, ABI 3700, ABI 3730, ABI 3730xl, ABI 3100, or ABI 3130. We have also recently added support for the MegaBACE sequencer family.
Comparison of the PeakTrace basecalling with ABI basecalling.
Common questions asked about PeakTrace
What is the difference between PeakTrace and LongTrace?
How is PeakTrace different to other basecaller like phred?
How do I use PeakTrace?
How much does PeakTrace FTP cost?
How much does PeakTrace:Box system cost?
Can I try PeakTrace before buying?
How do I purchase PeakTrace basecalling units?
Will you charge me for traces not improved by PeakTrace?
Will you keep my traces?
How does PeakTrace work?
I want to know more about PeakTrace?
Answers
What is the difference between PeakTrace and LongTrace?
The major difference is PeakTrace is a basecaller and trace processor while LongTrace is just a trace preprocessor. What this means in practice is that we can support a much wider range of trace types from all ABI sequencers, including even the ABI 377 and ABI 310.
If you have traces from an instrument that is supported by both LongTrace and PeakTrace (ie an ABI 3100, 3100 or 3730) then we suggest that you try both PeakTrace and LongTrace and see which one you prefer.
How is PeakTrace different to other basecaller like phred?
Other basecallers like phred or TraceTuner work by re-basecalling the processed peak data in the trace file. This means that there base calling accuracy is limited to the quality of processing provided by the ABI data collection software. PeakTrace is different in that it works on the raw data and involves reprocessing the raw data signal before basecalling. This means that we are able to provide a significantly better basecall with few errors and longer reads.
How do I use PeakTrace?
There are three ways to use PeakTrace. The first is to use the free version of PeakTrace which is designed for users with only a few traces to process. This provides exactly the same basecalling as the paid services, however, you are limited to processing only 10 traces per day.
If you need to process more traces then you will need to register for the high volume FTP PeakTrace service. Once registered you will need to purchase a number of PeakTrace basecalling units from our secure online store, or establish a standing account with us. You will be provided with a ftp account on our server where you can upload your traces to using any ftp program. Once your traces have been basecalled by the PeakTrace software you will be sent an email with the basecalling results. The final step is to log in to your ftp account once again and download the basecalled traces.
The third way is to use our standalone PeakTrace system, PeakTrace:Box. This is a full 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. For more information on PeakTrace:Box system please go to the PeakTrace:Box overview page.
If you want to visually compare the read length improvements offered by PeakTrace or LongTrace, we recommend you use a trace viewing application like ABI's Sequencing Analysis or Chromas.
How much does PeakTrace FTP cost?
The PeakTrace basecalling is sold on a per trace basis, however, we do not charge you unless the PeakTrace service improves your trace by at least five high quality (Q20+) bases. The current prices for the PeakTrace FTP basecalling service are:
| 100 PeakTrace Basecallings | $0.30 per trace | |
| 500 PeakTrace Basecallings | $0.26 per trace | |
| 2,000 PeakTrace Basecallings | $0.24 per trace | |
| 10,000 PeakTrace Basecallings | $0.20 per traces | |
| 25,000+PeakTrace Basecallings | Please contact |
How much does the PeakTrace:Box system cost?
The monthly lease prices for the PeakTrace:Box systems are:
- $900 for the 5000 trace per month system.
- $1200 for the 10,000 trace per month system.
- $2100 for the 25,000 per month traces system.
The major pricing difference between the PeakTrace:Box basecalling system and the FTP based system is that the box system does not come with the improvement guarantee, however, it is significantly cheaper on a per trace basis. We do also offer additional discounts are offered on the PeakTrace:Box system for long term contracts and/or higher volumes.
PeakTrace is slightly more expensive than LongTrace, however, it does offer greater improvements in read length and better basecalls over that obtained from LongTrace. Once again we suggest you try both (if you have an ABI 3730, 3100 or 3130) and see which one offers the greatest value.
Can I try PeakTrace for free?
Yes. We offer a 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 FTP and PeakTrace:Box systems. The only limitation with the free version is that you are limited to processing only 10 traces per day.
How do I purchase PeakTrace?
To purchase PeakTrace basecalling Units please visit our secure online shop. If expect to be basecalling over 5000 traces per month please as we offer very significant discounts for large standing orders.
To purchase the PeakTrace:Box system please .
Will you charge me for traces not improved by PeakTrace?
No. We automatically check the read length of each trace file basecalled by PeakTrace and only charge you for traces that are improved by at least five high quality (Q20+) bases. This means that you can upload complete traces folders without concern for being charged for failed DNA sequencing reactions or short runs. This guarantee does not apply to the PeakTrace:Box system as we do not know which traces have been improved by PeakTrace basecalling (the only way to do this would be to send your data to our server).
Will you keep my traces?
No. We have a very strict privacy policy regarding your data (please see our privacy policy for more details). We will never release your data to others, in fact, we will not examine your traces ourselves except with your written permission.
How does PeakTrace work?
PeakTrace is the result of seven years of R&D at Nucleics into improving DNA sequencing quality. While developing products like the CounterTrace DNA sequencing system, CounterTrace II DNA sequencing system and LongTrace we have learnt a great deal about how to best process and basecall the raw data in DNA sequencing traces. The algorithms that we have developed 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
Please visit the PeakTrace DNA sequencing overview page or the PeakTrace FAQ page. If you have any further questions please contact our or visit our PeakTrace forum to ask any question you may have.