Nucleics

Nucleics

Chromas 2.60 with PeakTrace Released

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Chromas with PeakTrace RP

Chromas 2.60 with PeakTrace

We are happy to announce the release, in collaboration with Technelysium, of PeakTrace for Chromas. Chromas 2.60 integrates the PeakTrace Basecaller into the Chromas trace viewer (enhance button). This release of Chromas comes with 20 free PeakTrace units allowing the power of PeakTrace to be explored during trace viewing on a trace by trace basis. Additional unit can be purchased via our secure PeakTrace Online Store.

Chromas 2.60 with PeakTrace can be downloaded for free from the Technelysium website.

Auto PeakTrace 6.41 Released

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PT_1000_june_2016

Example of PeakTrace Basecalling post base 1000.

We have released Auto PeakTrace 6.41. This release is an improvement/bug fix release and is a recommended update for all user of PeakTrace. The full list of changes include:

  • Improvements to the basecalling of traces containing mixed bases.
  • Improvements to clean baseline and extra baseline processing of traces.
  • Improved handling of traces that basecalled with the kb or peaktrace/kb options.
  • Improvements to mixed basecalling module.
  • Reduced memory requirements and increased processing speed.
  • Fix to the automated update so it works with Windows 10.
  • Static build of the associated runtime libraries avoiding missing .dll issues.

Auto PeakTrace 6.41 can be downloaded from the PeakTrace:Box Downloads page. If you do not have the password to access the downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it}.

If you are upgrading from a release before 6.20 then please see the How to upgrade to Auto PeakTrace 6 page for the upgrade requirements.

If you are updating from a version after Auto PeakTrace 6.20 then you will need to online activate again using your PeakTrace Serial Number.

Auto PeakTrace RP 6.41 Released

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Comparison between PeakTrace and KB basecallersWe have released Auto PeakTrace RP 6.41. This is a minor update, but with a number of important changes to the internal modules that improve the performance and basecalling quality. The full list of changes include.

  • Improvements to the basecalling of traces containing mixed bases.
  • Improvements to clean baseline and extra baseline processing of traces.
  • Improved handling of traces that are basecalled with kb or peaktrace/kb options.
  • Improvements to mixed basecalling module.
  • Reduced memory requirements and increased processing speed.

Auto PeakTrace RP 6.41 can be downloaded from our PeakTrace RP Downloads page for both Windows (XP, Windows 7, Windows 8 and Windows 10) and MacOS X (10.6+). It is also available via the in-app update function. If you do not have the password to access the downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier.

If you are not a current user of Auto PeakTrace RP 6 then please visit the Auto PeakTrace 6 RP registration page.

Auto PeakTrace 6.40 Released

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Auto PeakTrace 6.40 Options Window

Auto PeakTrace 6.40 Options Window.

We have released Auto PeakTrace 6.40 and PeakTrace 6.40 for Linux x86_64. This is a major release that improves the processing, basecalling, and appearance of traces. We have updated the Options menu of Auto PeakTrace 6 making it easier to use. We have also changed the the default settings to make the best use of the new features incorporated into this release and the Users Manual has been updated and improved. Finally, PeakTrace 6.40 has a new feature which allows the ABI Limits values to be set by PeakTrace instead of performing hard trimming of the trace files. The full list of changes

  • New Feature. Set ABI Limits option.
  • New Feature. Improved Options layout and default settings.
  • Improvements to the extra baseline setting to allow user control of the threshold for secondary peak removal.
  • Improvements to the clean baseline setting to allow user control of the threshold for removing trace noise.
  • Improved processing of traces generated using BigDye™ 1.1 chemistry.
  • Updated Help/Users manual.
  • Initial support of the NimaGen BrilliantDye™ Terminator chemistry.
  • Bug fixes and improvements.

The update is highly recommend for all user of Auto PeakTrace 6 or PeakTrace 6.  Both the Linux and Windows version of PeakTrace 6.40 can be downloaded from the PeakTrace:Box Downloads page. It is also available via the in-app update function within Auto PeakTrace 6. If you do not have the password to access the downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it}.

Auto PeakTrace RP 6.40 Released

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Auto PeakTrace RP 6.40 Options Menu

Auto PeakTrace RP 6.40 Options Menu

We have released Auto PeakTrace RP 6.40. The is a major update that significant improves trace quality output and appearance. We have changed the Options menu to make Auto PeakTrace RP easier to use and updated the default settings to make best use of the new settings. In addition, we have improved the help manual and added a new feature which allows the ABI Limits values to be set by PeakTrace instead of hard trimming. The full list of changes include.

  • New Feature. Set ABI Limits.
  • New Feature. Improved Options layout and default settings.
  • Improvements to the extra baseline setting to allow user control of the threshold for secondary peak removal.
  • Improvements to the clean baseline setting.
  • Improved processing of traces generated using BigDye 1.1 chemistry.
  • Updated Help manual.
  • Initial support of the NimaGen BrilliantDye™ Terminator chemistry.
  • Bug fix for the abi+kb output option.

This update is highly recommend for all user of Auto PeakTrace RP 6.30 or earlier. If you had been using the extra baseline setting with Auto PeakTrace 6.30 then you must upgrade to this version as the 6.30 version of extra baseline will no longer work.

Auto PeakTrace 6.40 can be downloaded from the PeakTrace RP Downloads page for both Windows (XP, Windows 7, Windows 8 and Windows 10) and MacOS X (10.6+). It is available via the in-app update function. If you do not have the password to access the downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it}.

If you are not a current user of Auto PeakTrace RP 6 then please visit the Auto PeakTrace 6 RP registration page.

Auto PeakTrace 6.30 Released

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Auto PeakTrace 6.30 Options Window

Auto PeakTrace 6.30 Options Window

We have released Auto PeakTrace 6.30. This is a major release incorporating two new features for improving trace appearance – extra baseline and secondary noise peak. In addition, a number of the underlying algorithms used in the PeakTrace basecalling process have been improved further enhancing trace processing quality and read length.

The full list of changes in Auto PeakTrace 6.30

  • New Feature. Extra baseline option for improved appearance of trace files.
  • New Feature. Secondary noise peak option to add peak noise to the traces.
  • Auto PeakTrace 6.30 requires CodeMeter runtime 6.20 or higher.
  • Improved trace processing quality and speed.
  • Unsupported run types now output .seq and .phd.1 files based on the KB basecall if these file types are requested.
  • Trace types which do not contain quality scores can now be output in ab1 format without quality scores if either clean baseline, extra baseline, or extra normalization is selected.
  • Additional check that the archive folder can be created when using the archive traces option.
  • Improved handling of traces processing when manually starting and stopping processing.
  • If the N base threshold is set to 1 or 0 and the fuse basecall value is greater than 0, then any N bases from the original KB basecall will be set to a quality score of 2.
  • Bug fixes and enhancements.

The release is recommended for all users of Auto PeakTrace earlier than 6.12 and is an optional update if you are running Auto PeakTrace 6.20. If you are using a release before 6.20 please contact us @ {This email is obscured. Your must have javascript enabled to see it} (or your local supplier) before installing as we will need to be provided with the PeakTrace Serial Number before you can use this update.

This update is available from the PeakTrace:Box Downloads page or if you are running Auto PeakTrace 6.20 it will be available from the built in update function of Auto PeakTrace.

Auto PeakTrace RP 6.30 Released

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apt_rp_630_options_window

We have released Auto PeakTrace RP 6.30. This is a major update with two new features – extra baseline and secondary noise peaks. These two setting can improve the appearance of the traces and help to better match the appearance of PeakTrace basecalled traces to that obtained from the KB Basecaller. These new features are explained in the user help manual, but we will also be writing in depth articles on each of these new features. The full list of changes include.

  • New Feature. Extra baseline option for improved appearance of trace files.
  • New Feature. Secondary noise peak option to add peak noise to the traces.
  • Unsupported run types now output .seq and .phd.1 files based on the KB sequence if these file types are requested.
  • The logfile now records the local time rather than the server time of processing.
  • Further improvements to increase the robustness of the software on very fast networks.
  • Additional check that the archive folder can be created when using the archive traces option.
  • Improved handling of traces processing when manually starting and stopping processing.
  • If the n base threshold is set to 1 or 0 and the fuse basecall value is greater than 0, then any N bases from the original KB sequence will be basecalled.
  • Upgrade of 7za to 15.14.
  • Bug fixes and other enhancements.

This PeakTrace RP release can be downloaded as per usual from the PeakTrace RP Downloads page for both MacOS X (10.6+) and Windows (XP, Windows 7, Windows 8 and Windows 10). It will be also be available via the in-app update function in a few days. If you do not have the password to access the downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it}.

If you are not a user of Auto PeakTrace RP 6 then please visit the Auto PeakTrace 6 RP registration page.

Auto PeakTrace RP 6.24 Released

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nucleics_10

We have released Auto PeakTrace RP 6.24. This update improves the robustness of Auto PeakTrace RP especially for user with fast networks. It is a recommended  that all user to upgrade to this release. The full list of changes are

  • Improvements to increase the robustness of the software on very fast networks.
  • Improved cleaning of temporary files from the Application Data folder.
  • Upgrade of cURL to 7.48.0.
  • Other minor bug fixes and enhancements.

This release can be downloaded from the PeakTrace RP Downloads page for both Windows (XP, Windows 7, Windows 8 and Windows 10) and MacOS X (10.6+) and automatically via the in-app update function. If you do not have the password to access the downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it}.

If you are not a current user of Auto PeakTrace RP 6 then please register on the Auto PeakTrace 6 RP registration page.

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 6.20 Released

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Auto PeakTrace Options Menu

We have release Auto PeakTrace 6.20. This is a major update that introduces a new licensing process – online activation. This update allows the PCR trim base to be manually set improving the sequencing of large PCR fragments (more than 500 bases). In addition, a large number of improvements have been made fixing bugs and enhancing the error messages. The full list of changes are:

  • New Feature. Online activation of Auto PeakTrace 6.
  • New Feature. User settable PCR trim base.
  • All N bases now have a quality score of 2 rather than 0.
  • Sporadic traces with all N bases should now not be generated.
  • Improved error messages with licenses that have not been upgraded to PeakTrace 6.00 or higher.
  • Other bug fixes and internal enhancements.

The release is recommended for all users of Auto PeakTrace earlier than 6.11 and is an optional update if you are running Auto PeakTrace 6.11 or 6.12. Please contact us @ {This email is obscured. Your must have javascript enabled to see it} (or your local supplier) before installing as we will need to be provided with the PeakTrace Serial Number before you can run this update.