What a year 2020 has been! Nucleics will be closing for our annual break over the Christmas/New Year period. We will be closed from the 21st December 2020 to the 4th January 2021.
Auto PeakTrace 6.95 & PeakTrace 6.95 Released
We have released Auto PeakTrace 6.95 and PeakTrace 6.95 for Windows & Linux. This is a major release that improves PeakTrace and is recommended for all users of the 6.94 or earlier series of PeakTrace. The server backend for Auto PeakTrace RP has also been updated to the latest release of PeakTrace.
The full list of changes.
- New Feature. Keep bubble spikes in the processed trace using the -ks option.
- New Feature. Auto PeakTrace 6 will check if you wish to save changes when exiting options window without manually saving.
- Improved mixed basecalling.
- Improved crosstalk correction on rare trace types.
- Improved processing and basecalling of traces with bubble spikes.
- Improved early basecalling.
- Bug fixes.
PeakTrace:Box customers can download the latest update from the PeakTrace:Box Downloads page. If you do not know the password to access the PeakTrace:Box Downloads page please contact us at support@nucleics.com or contact your local supplier for the update.
Auto PeakTrace 6.94 & PeakTrace 6.94 Released
We have released Auto PeakTrace 6.94 and PeakTrace 6.94 for Windows & Linux. This is a major release that improves PeakTrace and is recommended for all users of the 6.93 or earlier series of PeakTrace. The full list of changes.
- New feature. ABI377 and ABI310 .ab1 files are now output in .ab1 format with quality scores.
- New feature. Trace files without basecall or processed trace data can be output in .ab1 format using force processing setting.
- New feature. Support added for the following run conditions and instruments:
- ABI310
- 30cm POP4 BigDye 3 & 1
- 30cm POP6 BigDye 3 & 1
- 36cm POP4 BigDye 1
- 50cm POP6 BigDye 3 & 1 Rapid Run
- ABI3700
- POP6 BigDye 3 & 1
- POP5 BigDye 3 o ABI3130/3730
- 50cm POP7 ET terminator
- 50cm POP6 ET terminator
- ABI3130
- 80cm POP4 BigDye 3 & 1
- ABI3200
- 9kV BigDye 1
- 4kV BigDye 1
- MJResearch Biostation
- ABI310
- Default value for q average trim changed to 9 in a window of 40 bases.
- Default value for good base improvement changed to -10.
- Error code 25 description changed from “normalization failed” to “overload trace” to make cause of this result clearer.
- Improved mixed basecalling.
- Improved basecalling through “Dye Blob” regions.
- Improved processing of PCR product traces.
- Bug fixes.
PeakTrace:Box customers can download the latest update from the PeakTrace:Box Downloads page. If you do not know the password to access the PeakTrace:Box Downloads page please contact us @support@nucleics.com or contact your local supplier for the update.
Auto PeakTrace RP 6.94 Released
We have release Auto PeakTrace 6.94 for Windows & MacOSX (Mojave or earlier). This update incorporates a large number of changes and enhancements.
- New feature. ABI377 and ABI310 .ab1 files are now output in .ab1 format with quality scores.
- New feature. Trace files without basecall or processed trace data can be output in .ab1 format using force processing setting.
- New feature. Support added for the following run conditions and instruments:
- ABI310
- 30cm POP4 BigDye 3 & 1
- 30cm POP6 BigDye 3 & 1
- 36cm POP4 BigDye 1
- 50cm POP6 BigDye 3 & 1 Rapid Run
- ABI3700
- POP6 BigDye 3 & 1
- POP5 BigDye 3 o ABI3130/3730
- 50cm POP7 ET terminator
- 50cm POP6 ET terminator
- ABI3130
- 80cm POP4 BigDye 3 & 1
- ABI3200
- 9kV BigDye 1
- 4kV BigDye 1
- MJResearch Biostation
- ABI310
- Default value for q average trim changed to 9 in a window of 40 bases.
- Default value for good base improvement changed to -10.
- Error code 25 description changed from “normalization failed” to “overload trace” to make cause of this result clearer.
- Improved mixed basecalling.
- Improved basecalling through “Dye Blob” regions.
- Improved processing of PCR product traces.
- Bug fixes.
Auto PeakTrace RP 6.94 can be downloaded from the PeakTrace RP Downloads page. If you do not know the password to access the PeakTrace RP Downloads page please contact us or your local supplier for the update.
Christmas & New Years Holiday at Nucleics 2019
What another huge year 2019 has been! Nucleics will be shutting down for our annual company holiday (vacation) break over the Christmas/New Year period while we all relaxing at the beach. We will be closed from the 17th December 2019 until 6th January 2019. I (Daniel) will be checking my emails occasionally over this time, but it might take us longer than usual to get back to you.
Auto PeakTrace 6.934 & PeakTrace 6.934 Released

Auto PeakTrace 6.934 Overview
We have released Auto PeakTrace 6.934 and PeakTrace 6.934 for Windows & Linux. This is a small bug fix release that corrects an issue with the simple mixed basecall as well as a rare thread race issue when archive traces and auto start are both selected. Unless you are using simple mixed basecall (nobody should be as it is inferior to standard mixed basecalling), this update is optional.
The Auto PeakTrace RP and PeakTrace for Chromas changes are all on the server side so there will not be a corresponding update for these programs.
PeakTrace:Box customers can download the latest update from the PeakTrace:Box Downloads page. If you do not know the password to access the PeakTrace:Box Downloads page please contact us @support@nucleics.com or contact your local supplier for the update.
Why use PeakTrace?

Comparison between the KB & PeakTrace Basecaller
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 doing 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.
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.
If you would like to learn more about how PeakTrace can save you money and increase your DNA sequencing business then please contact our sales team @ {This email is obscured. Your must have javascript enabled to see it}.
In depth look at the new features of PeakTrace 6
PeakTrace 6 (Auto PeakTrace 6, Auto PeakTrace 6 RP and the Linux PeakTrace 6) has a number of very powerful options that may not have been explored by many users of older versions of PeakTrace. We understand that most of our customers are busy running a sequencing facility and so don’t always have the time to look into each new PeakTrace feature on release. To help we are creating a new series of posts looking in depth what these new options can do, how they can best be used, and how they can help our customers make the most of PeakTrace.

Auto PeakTrace 6.932 Options
The first in this series of in depth posts is on the Clean Baseline setting and when you may want, and not want, to use this setting. The options we will be covering include
- Automatic Bubble Spike Removal
- Extra Normalization
- Extra Smoothing Part I
- Extra Smoothing Part II
- Trim 3′ End Only
- Mixed Basecalling and Simple Mixed Basecalling
- Picket Fence Trace Basecalling
- Trace Reports
- Clean Baseline
- PCR Trim Base
- Extra Baseline
- Secondary Noise Peaks
- Set ABI Limits
- Use Edited Basecalls
- Skip Short Traces
- PeakTrace Basecalling with KB Fallback
- Fuse Trace and Fuse Basecall
- No Peak Resolution
- Q Average Trace Trimming
- Input Overwrite
We will also be covering some of the more abused/misunderstood settings within Auto PeakTrace 6 such as
Auto PeakTrace 6.933 & PeakTrace 6.933 Released

Auto PeakTrace 6.933 Overview
We have released Auto PeakTrace 6.933 and PeakTrace 6.933 for Windows. This is a small bug fix release that fixes rare issues identified by some of our customers. If you are not experiencing any issues with your traces then this update is optional. We aim to always have no known bugs in the latest versions of PeakTrace and will release an update as soon as any issues are identified and fixed.
The Linux version will be released in the coming days and the improvements will be incorporated automatically into the Auto PeakTrace RP and PeakTrace for Chromas versions as the changes are all on the server side.
PeakTrace:Box users can download the latest update from the PeakTrace:Box Downloads page. If you do not know the password to access the PeakTrace:Box Downloads page please contact us @support@nucleics.com or contact your local supplier for the update.
Auto PeakTrace 6.932 & PeakTrace 6.932 Released

Auto PeakTrace 6.932 Options
We have released Auto PeakTrace 6.932 and PeakTrace 6.932 for Linux and Windows. This is a small bug fix release that resolves issues on rare trace types, especially short PCR reads. We would like to thank those of our customers who sent us examples .ab1 files containing potential issues. Our policy is to never have known bugs in the latest release and once we are made aware of an issue we aim to rectify it as soon as possible (usually within weeks). If you notice any trace not being processed and basecalled as you expect, or any other issue of concern, then please get in contact with us.
For users of PeakTrace RP the changes have been automatically made on the remote server side so there is no need to upgrade.
PeakTrace:Box users can download the latest update from the PeakTrace:Box Downloads page. If you do not know the password to access the PeakTrace:Box Downloads page please contact us @support@nucleics.com or contact your local supplier for the update.
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