Nucleics

Nucleics

Auto PeakTrace 6.62 & PeakTrace 6.62 Released

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Auto PeakTrace 6.62 Options

Auto PeakTrace 6.62 Options

We have released another small update for Auto PeakTrace and PeakTrace (6.62). This adds improved support for the BrilliantDye™ chemistry when run on the ABI 3730 with 50cm arrays and the standard 8.5.kV run voltage. It also include improve identification of mixed traces during processing. This change has been included on the server side for Auto PeakTrace RP so there is no need to update for RP users.

Auto PeakTrace 6.62 can be downloaded from the PeakTrace:Box Downloads page. If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update. The command line PeakTrace versions for Windows and Linux are also available.

This update is a optional update for all current users of the PeakTrace:Box System.

Auto PeakTrace 6.61 & PeakTrace 6.61 Released

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Auto PeakTrace 6.61 Options window

Auto PeakTrace 6.61 Options window

We have released a small update for Auto PeakTrace and PeakTrace (6.61). This corrects an error in the handling of .seq files when skip short traces and set abi limits is used when no trace trim function is used. This bug has been corrected on the server side for Auto PeakTrace RP.

Auto PeakTrace 6.61 can be downloaded as usual from the PeakTrace:Box Downloads page. If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update. The command line PeakTrace versions for Windows and Linux are also available.

This update is a recommended update for all current users of the PeakTrace:Box System.

Auto PeakTrace RP 6.60 Released

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Auto PeakTrace RP 6.60 Options window

Auto PeakTrace RP 6.60 Options window

We have released Auto PeakTrace RP 6.60 for Windows (XP to Win 10) and MacOS X (10.6+). This major upgrade improves trace processing, appearance and basecalling quality.

This release is an essential upgrade for all uses of Auto PeakTrace RP as it introduces a breaking change for the set abi limits option. Users that don’t upgrade will no longer to be able to hard trim traces.

In addition to changing the default value for the set abi limits option, PeakTrace 6.60 introduces a new basecaller setting – reltrace. The reltrace option outputs the raw data baseline, slightly smooth and mobility shifted with either the original KB basecall or the PeakTrace basecalled trace. The setting is useful if you wish to obtain data as close to the raw data as possible avoiding all the data manipulation that both KB and PeakTrace normally perform. This setting is useful if you wish to use the peak height data to perform downstream data analysis since the relatively peak heights in the output will match those observed in the raw data.

The full list of changes include.

  • New Feature. RelTrace. This outputs a usable raw data chromatogram that can be used with downstream applications to detect polymorphisms.
  • New Feature. Use of set abi limit without trimming outputs trace file without removing non-basecalled region.
  • New Feature. .seq files are output with trace trimming when set abi limits on.
  • New Default. The set abi limits is now on.
  • New Error Code: 23. KB fallback failed.
  • Improved trace processing that avoids suppression of large secondary peaks.
  • Improved basecalling.
  • Improved trace normalization.
  • Improved mixed basecalling.
  • Improved fuse basecall.
  • Improved processing of true profile traces.
  • Improved detection and processing of PCR product and weak signal traces.
  • ABI/KB basecalled traces no longer have adjustments to the quality scores.

Auto PeakTrace RP 6.60 for Windows and MacOS X can be downloaded from the PeakTrace RP downloads page. This release will soon be available via automatic update and is a CRITICAL upgrade for all users of Auto PeakTrace RP.

If you require the password to access the PeakTrace RP downloads page please contact us @{This email is obscured. Your must have javascript enabled to see it} or your local supplier.

Auto PeakTrace 6.60 & PeakTrace 6.60 Released

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PeakTrace 6.60 Example at base 1200

PeakTrace 6.60 example near base 1200

We have released Auto PeakTrace 6.60 and PeakTrace 6.60 for Windows & Linux. This is a major upgrade that involved the improvement of many aspects of the PeakTrace Basecaller to improve the trace output and basecalling.

The most significant change in 6.60 is the introduction of a new basecaller output – RelTrace. This outputs the raw peak data mobility shifted, baselined, and the ccd detector noise removed along with either the KB Basecaller or PeakTrace basecalls. This setting is ideal for applications requiring measurement of the true relative peak heights such as polymorphism or methylation studies where the normal processing provided by PeakTrace or KB basecallers will distort the true relative peak heights.

The full list of changes in this version include:

  • New Feature. RelTrace basecaller output.
  • New Feature. Use of set abi limit without trimming outputs trace file without removing the non-basecalled regions.
  • New Feature. The .seq files are output with trace trimming when set abi limits on.
  • New Default. The set abi limits is now on.
  • New Error Code. 23. KB fallback failed.
  • Improved trace processing that avoids suppression of large secondary peaks.
  • Improved trace normalization.
  • Improved processing of true profile traces.
  • Improved basecalling.
  • Improved mixed basecalling.
  • Improved fuse basecall.
  • Improved detection and processing of PCR product and weak signal traces.
  • ABI/KB basecalled traces no longer have adjustments to the quality scores.
  • Update of the CodeMeter runtime to 6.50a.

Auto PeakTrace 6.60 can be downloaded as usual from the PeakTrace:Box Downloads page. If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update. The command line PeakTrace versions for Windows and Linux are also available.

This update is a recommended update for all current users of the PeakTrace:Box System.

Auto PeakTrace 6.53 Released

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We have released an update for Auto PeakTrace (6.53). The release improves peak and trace normalization.

  • Improved peak normalization of traces especially those derived from PCR products and/or traces where set abi limits has been used.
  • Improved extra normalization of traces derived from PCR products to avoid normalization of the noise regions after the trace signal ends.

It is possible that the PeakTrace Serial Number will need to be entered again after installation. If so, just press the back button on the registration window and enter your existing serial number.

Auto PeakTrace 6.53 can be downloaded as usual from the PeakTrace:Box Downloads page. If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update. We will also be updating the commandline PeakTrace versions for Windows and Linux in the next few days.

Auto PeakTrace 6.52 Released

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We have released a small update for Auto PeakTrace (6.52) to fix a bug in the copy other files option introduced in Auto PeakTrace 6.47 that prevented the non .ab1 files from being copied to the output folder when located in sub-folders. This bug only affects Auto PeakTrace on Windows and is optional if you are not using the copy other files setting.

This release also updates the required CodeMeter Runtime to 6.40b. This release from Wibu fixes a bug specific for Windows XP users that may cause the license to no longer work.

It is possible that the PeakTrace Serial Number will need to be entered again after installation. If so, just press the back button on the registration window and enter your existing license serial number.

Auto PeakTrace 6.52 can be downloaded as usual from the PeakTrace:Box Downloads page. If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update.

Auto PeakTrace 6.51 Released

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We have released a small optional update to Auto PeakTrace (6.51) as a work around to a bug recently introduced in the CodeMeter runtime. This bug only affects Auto PeakTrace on Windows.

If you have already upgraded to Auto PeakTrace 6.50 then you only need to install this update if we advise you to do so. For anyone using a version of Auto PeakTrace before 6.50 we strongly encourage you to update to this release.

Auto PeakTrace 6.51 can be downloaded as usual from the PeakTrace:Box Downloads page. If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update.

Auto PeakTrace 6.50 & PeakTrace 6.50 Released

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Auto PeakTrace 6.50 Options Window

Auto PeakTrace 6.50 Options Window

PeakTrace 6.50 for Linux, PeakTrace 6.50 for Windows, and Auto PeakTrace 6.50 have been released. This update improves the performance and accuracy of PeakTrace and incorporates improvements to the QualTrace III Trace Reports to make them independent of PeakTrace. This release is a recommended update for all users of PeakTrace. The full list of changes

  • New Feature. QualTrace III only Trace Reports.
  • Improvements to mixed basecalling to reduce the false negative rate.
  • Improvements to the processing of short traces to increase trace read length.
  • Improvements to the fuse trace module.
  • The .scf file now records the correct basecaller if stealth mode or abi/kb basecaller options are used.
  • Update of CodeMeter runtime to 6.40a.

PeakTrace 6.50 for Linux, PeakTrace 6.50 for Windows, and Auto PeakTrace 6.50 can be downloaded as usual from the PeakTrace:Box Downloads page. The automatic update for Auto PeakTrace will be released in the coming days.

The two command line versions (PeakTrace 6.50 for Windows or Linux) require a password to unzip the files so please contact us @ {This email is obscured. Your must have javascript enabled to see it} or your local supplier for the archive password (this is different to the password to access the downloads page). You will need to download and use the free program 7zip to unzip the archives.

If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update. This update will also be available via the automatic update system soon if you are using PeakTrace 6.20 or higher.

If you are currently running a version of PeakTrace from before 6.10 you will also need a license upgrade and/or the PeakTrace Serial Number. Please contact us to obtain these updates.

The changes and improvements of this release have also been provided to the RP servers so users of Auto PeakTrace RP will obtain them automatically.

Auto PeakTrace & PeakTrace 6.47 Released

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Auto PeakTrace 6.47, PeakTrace 6.47 for Windows, and PeakTrace 6.47 for Linux x86_64 have been released. This update is a bug fix and optimisation release that resolves a number of outstanding bug and small annoyances. It is a recommended update for all users of PeakTrace 6.40 or greater.

  • Improvements to Auto PeakTrace prevent the reading of the empty dot file created when copying files from Mac OS to Windows drive.
  • Improvements to no peak resolution option.
  • Improvements to the mixed basecalling module.
  • QualTrace III analysis is not turned off by corrupt .ab1 files.
  • Force processing will now PeakTrace basecall traces where the fuse trace or fuse basecall fails.
  • Fixed a bug which prevented TraceTuner basecalling working on Windows 8.1 and higher.
  • Fixed a bug which caused input overwrite to not work with Auto PeakTrace.
  • Fixed a bug which caused an inaccurate basecall improvement when using set abi limits.
  • Fixed a bug that prevents short traces being reprocessed through KB after PeakTrace basecalling.
  • Fixed a bug with the trace processor reported in .phd.1 files.
  • Update of the required CodeMeter runtime to 6.40.

Auto PeakTrace 6.47, PeakTrace 6.47 for Windows, and PeakTrace for 6.47 for Linux x86_64 can be downloaded from the PeakTrace:Box Downloads page.

The two command line versions (PeakTrace 6.47 for Windows or Linux) require a password to unzip the files so please contact us @ {This email is obscured. Your must have javascript enabled to see it} or your local supplier for the archive password (this is different to the password to access the downloads page). You will need to download and use the free program 7zip to unzip the archives.

If you do not have the password to access the PeakTrace:Box Downloads page please contact us @ {This email is obscured. Your must have javascript enabled to see it} or contact your local supplier for the update. This update will also be available via the automatic update system soon if you are using PeakTrace 6.20 or higher.

If you are currently running a version of PeakTrace from before 6.10 you may also need a license upgrade and/or the PeakTrace Serial Number.

Auto PeakTrace RP 6.47 Released

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We have released Auto PeakTrace RP 6.47. We have spent the last month chasing down and fixing a series of annoying bugs with the aim of improving PeakTrace. The full list of fixes and improvements are:

  • Improvements to prevent the reading of the empty dot file created when copying files from a MacOS X to Windows drive.
  • Improvements to the no peak resolution module.
  • Improvements to the mixed basecalling module.
  • Force processing will now force the use of the PeakTrace basecaller where the fuse trace or fuse basecall fails due to major differences between the KB and PeakTrace basecalls.
  • Fixed a bug which caused an inaccurate basecall improvement value to be reported when using set abi limits.
  • Fixed a bug that prevents short traces (under 250 bases) being reprocessed through KB after PeakTrace basecalling.
  • Fixed a bug with the trace processor that was reported in the .phd.1 files.
  • Fixed bug where an error message was displayed if the RP license code had not yet been entered.
  • Update of cURL to 7.51 and 7za to 16.04.

Auto PeakTrace RP 6.47 for Windows and MacOS X can be downloaded from the PeakTrace RP downloads page. This release will soon be available via automatic update and is a recommend upgrade for all users of Auto PeakTrace RP.

If you require the password to access the PeakTrace RP downloads page please contact us @{This email is obscured. Your must have javascript enabled to see it} or your local supplier.