A question we get asked frequently is why should a core facility or sequencing service company use the PeakTrace Basecaller™ — after all the KB Basecaller™ works well and is effectively free since it comes with the DNA sequencer?
This is a really good question, because although the PeakTrace Basecaller is very cheap (a few cents per trace at scale), it is still an extra cost and most facilities are always looking for ways to save every cent they can.
The simple answer is that not only will PeakTrace give your customers longer reads and better traces, it will make you money if used intelligently.
Here are the top ten reasons everyone performing Sanger DNA sequencing should be using PeakTrace.
1. The improved appearance and longer reads provided by PeakTrace attracts new customer and retain old customers
Facilities that use PeakTrace have happier customers who send them more samples. Given that most of the costs of running a DNA sequencing service are fixed, it only takes a small increase in sequencing volume to make a big difference to your bottom line. We have seen time and time again that keeping your customers happy by providing them with the best results possible will bring in additional business. It only takes a couple of extra trays a month to more than pay for PeakTrace.
2. Sanger DNA sequencing is not going away any time soon
Despite all the interest and investment in Next-Gen sequencing, Sanger is here to stay. If you are doing Sanger sequencing, you should be using the best tools available and PeakTrace is the best basecaller. If you are currently using the KB Basecaller because you think it is better than the old ABI Basecaller, then you care about sequencing quality. If you care about quality, you should be using PeakTrace.
3. Your competitors are already using PeakTrace (mostly in secret) to gain a massive advantage in the market place
The DNA sequencing market is extremely competitive. If you don’t offer the best basecalling results to your customers by using PeakTrace, they will leave you for a service that does use PeakTrace. Do you really want to lose your customers over something that is so easy and cheap to fix? Once again, the high fixed costs involved in offering a sequencing service make the loss of any business very expensive to your bottom line.
4. You pay only for success
Unlike everything else in DNA sequencing, you only pay for those traces that are improved by PeakTrace. ThermoFisher (ABI) won’t give you a refund on the BigDye™ or the POP7™ polymer if your sequencing reaction fails, but we do. Because not every reaction is a success, the actual cost of using PeakTrace is even cheaper than it appears (a few cents per trace) when used at volume.
5. PeakTrace can rescue low quality sequence data
While PeakTrace is designed to make good traces better, it can also improve some bad traces enough to make them acceptable. Any trace that can be rescued by PeakTrace is one sequencing sample that does not need to be repeated, thus saving your facility and customers time and money.
6. PeakTrace’s polymorphic base (mixed peaks) detection is better
One important feature of PeakTrace is it can more accurately identify and quantify polymorphic (mixed peak) positions. The mixed base detection in PeakTrace makes fewer errors differentiating true mixed peaks from false mixed peaks caused by noise or overlap than the KB Basecaller. Traces with the true (raw channel) relative peak heights can also be output easily from PeakTrace using the no peak resolution option. This option enables accurate quantification of the peak height ratios. Since PeakTrace 6.96, .poly files can be generated aiding in the detection of polymorphic basecalls.
7. PeakTrace can be used on instruments where KB is not available
If you own an ABI 310 (or even ABI 377) you can still use PeakTrace. You not only get the improved read length and trace appearance, but also quality scores for all the basecalls. Why pay to update to a new sequencer to just use the KB Basecaller when your current machine can be upgraded cheaply by just using PeakTrace?
8. PeakTrace can be used to increase DNA sequencer throughput
Nucleics has developed a set of run modules that enable a user of PeakTrace to obtain the same read length provided by KB, but in less than half the run time. This effectively doubles the number of sequencing instruments you have on demand, or enables you to reduce the number of sequencers you need to meet your demand. If you now have two machines, you can sell one and still get the same throughput out of just one single machine. This could save you tens of thousands of dollars a year or allow you to meet demand spikes quickly.
9. PeakTrace can extend the life of the array
One little known feature of PeakTrace is it can allow you to get more runs out of the array before it needs a change. While of course it will dependent on the actual lab condition and standards, but many of our customers are using the arrays for twice the number of runs they can achieve using the KB Basecaller.
10. PeakTrace comes with a 60 day, full money back guarantee
If you find that the PeakTrace Basecaller does not meet your expectations for any reason you can return it within 60 days for a full refund – all we ask is that you tell us why you chose to cancel. Try PeakTrace without fear that it won’t work in your facility.