Nucleics

Nucleics

Auto PeakTrace RP 6.23 Released

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PeakTrace_example

We have released Auto PeakTrace RP 6.23. This is a minor update that helps the software overcome network issues. We have found that some of our users have poorly configured networks that prevent the Auto PeakTrace RP software from being able to upload trace files to the remote RP server. This update improves the robustness of the software to such networks.

This update is only recommend for users of Auto PeakTrace RP 6.22 if you are having trouble connecting to the remote RP server. It can be downloaded from the PeakTrace RP Downloads page for both Windows (XP, Win7, Win8 and Win 10) and MacOS X (10.6+). If you do not have the password to access this page please contact@ {This email is obscured. Your must have javascript enabled to see it}. If you are a new user of Auto PeakTrace RP 6 then please register at our Auto PeakTrace 6 RP registration page.

Auto PeakTrace RP 6.22 Released

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Auto PeakTrace RP 6.22 Options Window

Auto PeakTrace RP 6.22 has been released. The major change in this release is the ability to set the PCR base beyond 500. This allows better trimming of the end of PCR fragment traces larger than 500 bases. The full list of changes includes

  • New Feature. User settable PCR trim base.
  • All N bases now have a quality score of 2 rather than 0.
  • Improved handling of licensing issues.
  • Bug fixes and enhancements.

It is recommend that all users of Auto PeakTrace RP 6.20 or higher upgrade to this version. It can be downloaded from the PeakTrace RP Downloads page for both Windows (XP, Win7, Win8 and Win 10) and MacOS X (10.6+). If you do not have the password to access this page please contact@ {This email is obscured. Your must have javascript enabled to see it}. If you are a new user of Auto PeakTrace RP 6 then please register at our Auto PeakTrace 6 RP registration page.

Auto PeakTrace RP 6.21 Released

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Auto PeakTrace RP 6.21 has been released. This is update improves the reliability and speed of PeakTrace RP processing.

  • New Feature. Additional Australian and Chinese based RP server.
  • More accurate estimated time to completion function.
  • Improved handling of proxy server issues.
  • Bug fixes.

It is highly recommend that all current users of Auto PeakTrace RP upgrade to this version. It can be downloaded from the PeakTrace RP Downloads page for both Windows (XP, Win7, Win8 and Win 10) and MacOS X (10.6+). If you do not have the password to access this page please contact@ {This email is obscured. Your must have javascript enabled to see it}. If you are a new user then please register to use Auto PeakTrace 6 RP.

Auto PeakTrace RP 6.20 Released

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APT_RP_620_options

Auto PeakTrace RP 6.20 has been released. This is a major upgrade designed to improve processing speed. The file uploading and server backed has been completely redesigned to be able to dynamically adapt to your network speed. In addition we have added new servers on the USA West Coast (Los Angeles), USA East Coast (Atlanta) and Europe (Netherlands). We will be adding new servers in the coming months in both China and Singapore. The full list of changes are:

  • New Feature. Regional based servers to improve processing speed. Use of the new servers may require a new license code.
  • New Feature. User control over file upload encryption. Turning off encryption can speed the upload speed.
  • Dynamic speed adjustment to match upload speed with network speed. This should result in much faster trace processing on fast networks.
  • Bug fixes and internal improvements to improve robustness.

It is highly recommend that all current users of Auto PeakTrace RP upgrade to this version. It can be downloaded from the PeakTrace RP Downloads page for both Windows (XP, Win7, Win8 and Win 10) and MacOS X (10.6+). If you do not have the password to access this page please contact@ {This email is obscured. Your must have javascript enabled to see it}. If you are a new user then please register to use Auto PeakTrace 6 RP.

Update: PeakTrace Software Download Page

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We have updated the layout of our software downloads page. Previous we all software updates were on the same page for the different versions of PeakTrace, but we found that many customers were confused as to which version they should download. To try and make this process less confusing we have split the downloads pages into an PeakTrace RP Downloads page and a PeakTrace:Box Downloads page.

These pages are also direct accessible from the Support menu.

The passwords to access these pages has changed so if you wish to download an update just send email us at  {This email is obscured. Your must have javascript enabled to see it}.

Auto PeakTrace RP and the Good Base Improvement Setting

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Just a quick update on how Auto PeakTrace RP charges for traces processed. Officially it has always been that if you set the good base improvement to value great than −10 (i.e −9 and higher) then you would be charged for traces that are not improved by PeakTrace. This rule was to stop the abuse of the PeakTrace server, as well as to encourage users to set sensible values (the default −20 is best). Setting the good base improvement to value higher than −10 is far from optimal.

We have until now not enforced this rule, but unfortunately some people have not used this freedom sensibly and so we have reluctantly started enforcing this rule. If you have been using a good  base improvement value of greater than −10 then we highly recommend setting it back to a value below this (i.e. the default −20 is best).

One final tip. If you are having problems entering a negative number in the good base improvement box you can do it by pressing the reset button on the options window and then modifying the number, or by copy and pasting in the negative value from a text document. We will be making it easier to enter a negative number for this value in the next release.

Auto PeakTrace RP 6.10 Software Released

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Auto PeakTrace 6 RP 6.10 Options Window

Auto PeakTrace RP Options Window.


We have released Auto PeakTrace RP 6.10. This is a major update to our PeakTrace RP software and offers a number of improvement and new features that have resulted from our customer’s suggestions as well as the usual bug fixes. The full list of changes are.

  • New Feature. Manual control of the skip short base threshold.
  • New Feature. Limit trimming to the 3′ end of the trace only.
  • New Feature. Set use of the edited basecalls within the trace.
  • New Feature. Set the output to overwrite the input traces.
  • New Feature. Picket Fence trace output.
  • New Feature. PeakTrace basecalling with KB fall back.
  • New Feature. Simple mixed basecalling.
  • A reorganized and simplified Options window.
  • Improved fuse trace of repeat sequence regions.
  • Improved fuse basecall of repeat sequence regions.
  • Improved basecalling of mixed peaks.
  • Bug fixes.

I will be writing posts on the new features over the coming weeks as they provide some very interesting and useful features.

This major update is available from the Nucleics Downloads page and it is highly recommend that all users of PeakTrace RP upgrade to this version.