Nucleics

Nucleics

Auto PeakTrace 6.931 Released

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We have released Auto PeakTrace 6.931 and PeakTrace.exe 6.921 for Windows. This minor update fixes two issue that can cause PeakTrace to crash on rare occasions.

These bugs fixes have been made possible by customers sending us example .ab1 files that have caused issues. If you experience any issues please send us example trace(s) as tracking down bugs that cause a crash once every 100,000 traces is much easier for us if we have an example file. Our aim is to always have zero known bugs in all new releases.

This update is a recommend upgrade for all users PeakTrace customers since the bugs that have were fixed have been present for more than 12 months.

Auto PeakTrace 6.931 can be downloaded 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 6.93 Released

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Auto PeakTrace 6.93 Options

Auto PeakTrace 6.93 Options

We have released Auto PeakTrace 6.93. This update improves the control of Auto PeakTrace from the command line and brings it into parity with the peaktrace.exe command line version. It is recommend that all users of peaktrace.exe change to using Auto PeakTrace as peaktrace.exe will not be updated in the next major release of PeakTrace. The full list of changes includes.

  • New Feature. Command line control of QualTrace III options.
  • New Feature. Command line control of the manual override settings.
  • New Feature. Command line control of the proxy server settings.
  • New Feature. Custom PeakTrace and QualTrace log file names and paths can be set from the command line.
  • New Feature. Auto PeakTrace can be run in watch mode checking for new .ab1 file in input folder from the command line.
  • New Feature. Control of message output to the command line window via -sl option switch.
  • New Feature. The header line can be removed from log files with -sh option on the command line.
  • New Feature. Support added for ABI3130 80cm array POP7 runs.
  • If Auto PeakTrace crashes in command line mode it will restart in command line mode, but not output any message to the command window.
  • CodeMeter runtime requirement upgraded to 6.80.
  • Minor bug fixes

Auto PeakTrace 6.93 can be downloaded 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.

PeakTrace 6.92 Command line Versions Released

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Comparison between the KB & PeakTrace Basecaller

Comparison between the KB & PeakTrace Basecaller

We have released the PeakTrace 6.92 command line versions for Windows and Linux. The full list of changes include

  • New Feature. Calculation of the signal start peak location directly from the trace.
  • New Feature. Controlled removal of minor peaks without mixed basecalling.
  • Support for additional run conditions including ultra low voltage runs.
  • ABI 377 support added.
  • Improved basecalling.
  • Improved basecalling of PCR product traces.
  • Improved mixed basecalling.
  • Improved processing of traces with polymorphic peaks.
  • Improved processing of traces with long single base runs.
  • Improved trace trimming.
  • Improved removal of air bubble spikes in the trace.
  • Improved clean baseline and extra baseline processing.
  • CodeMeter runtime requirement upgraded to 6.70a.

PeakTrace 6.92 can be downloaded 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.

If you are using PeakTrace on windows it is highly recommended that users transition to using the command line feature of Auto PeakTrace 6.92.

Auto PeakTrace 6.92 Released

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Auto PeakTrace 6.92 Overview

Auto PeakTrace 6.92 Overview

We have released Auto PeakTrace 6.92. This update supports a new method of controlling the removal of minor peaks from under major peaks as well of hundreds of small changes that add up to a major improvement to trace appearance and basecalling. The full list of changes includes.

  • New Feature. Calculation of the signal start peak location directly from the trace.
  • New Feature. Controlled removal of minor peaks without mixed basecalling.
  • Support for additional run conditions including ultra low voltage runs.
  • ABI 377 support added.
  • Improved basecalling.
  • Improved basecalling of PCR product traces.
  • Improved mixed basecalling.
  • Improved processing of traces with polymorphic peaks.
  • Improved processing of traces with long single base runs.
  • Improved trace trimming.
  • Improved removal of air bubble spikes in the trace.
  • Improved clean baseline and extra baseline processing.
  • CodeMeter runtime requirement upgraded to 6.70a.

Auto PeakTrace 6.92 can be downloaded 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.

The command line version of PeakTrace for Windows and Linux will be released in the coming days, however, it is highly recommended that all Windows command line users transition to using the command line feature of Auto PeakTrace 6.92.

Auto PeakTrace RP 6.92 Released

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Auto PeakTrace RP 6.92

Auto PeakTrace RP 6.92

We have release Auto PeakTrace 6.92 for Windows. This update that supports a new method of removing minor peaks from under the major peaks, as well as many changes on the server side to improve processing and basecalling. The full list of changes includes.

  • New Feature. Calculation of the signal start peak location directly from the trace.
  • New Feature. Controlled removal of minor peaks without mixed basecalling.
  • Support for additional run conditions including ultra low voltage runs.
  • ABI 377 support.
  • Improved basecalling.
  • Improved basecalling of PCR product traces.
  • Improved mixed basecalling.
  • Improved processing of traces with polymorphic peaks.
  • Improved processing of traces with long single base runs.
  • Improved trace trimming.
  • Improved removal of air bubble spikes in the trace.
  • Improved clean baseline and extra baseline processing.
  • Many additional small bug fixes and enhancements.

Auto PeakTrace RP 6.92 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. The MacOS X version will be released in the coming days.

PeakTrace 6.92 Released

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KB PeakTrace Comparison

We have released PeakTrace 6.92. This is a bug fix and enhancement release and is the culmination of six months hard work by the team at Nucleics. We have gone through nearly every line of code within PeakTrace to improve and enhance the processing and basecalling of Sanger sequencing traces. While there is no single massive changes from all this work, the cumulative effect of all these small changes adds up to a major improvement. The full list of changes includes.

  • Support for additional run conditions including ultra low voltage runs.
  • ABI 377 support.
  • Improved basecalling.
  • Improved basecalling and processing of PCR product traces.
  • Improved mixed basecalling.
  • Improved processing of traces with polymorphic peaks.
  • Improved processing of traces with long single base runs.
  • Improved trace trimming.
  • Improved removal of air bubble spikes in the trace.
  • Improved clean baseline and extra baseline processing.

PeakTrace 6.92 is live on our servers so our PeakTrace RP users will be automatically getting the benefits of 6.92. Over the coming week we will be releasing updates for the standalone PeakTrace:Box for Linux and Windows, along with an update for the Auto PeakTrace RP client program for Windows and MacOSX. We will make further announcements when these updates are released.

Auto PeakTrace 6.91 and PeakTrace 6.91 released

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Auto PeakTrace 6.91

Auto PeakTrace 6.91

We have released Auto PeakTrace 6.91 and PeakTrace 6.90 for Linux. This release is a minor bug fix release for 6.90 and is a recommend update for all uses of PeakTrace 6.90. Other than bug fixes this release does not contain any changes from 6.90.

Auto PeakTrace 6.91 and PeakTrace 6.91 for Linux can be downloaded 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.

The command line version of PeakTrace for Windows will be released in the coming days, however, it is highly recommended that all Windows command line users transition to using the command line feature of Auto PeakTrace 6.91.

 

Auto PeakTrace RP 6.91 Released

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Auto PeakTrace 6 RP 6.91

Auto PeakTrace 6 RP 6.91

We have released Auto PeakTrace 6 RP 6.91 for Windows and MacOS X. This update is an “under-the-hood” update move our primary development platform from Windows XP to Windows 10. Auto PeakTrace RP still supports Windows XP, but by updating we aim to improve the performance and compatibility of PeakTrace with newer version of the Windows OS. The full list of changes include.

  • New Feature. x64 version.
  • New Feature. High DPI monitor support.
  • New PeakTrace installer.
  • Further improvements to the processing and basecalling of weak traces.
  • 7za updated to 18.05.
  • cURL updated to version 7.59.0.
  • Wine updated to 2.2 for the MacOSX release.
  • Other minor bug fixes and enhancements.

Auto PeakTrace RP 6.91 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.

Auto PeakTrace & PeakTrace 6.90 Released

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Auto PeakTrace 6.90 Options Window

Auto PeakTrace 6.90 Options Window

We have released Auto PeakTrace 6.90 and PeakTrace 6.90 for both Linux and Windows. This release contains a major overhaul of all the algorithms used in PeakTrace with the aim to improve low quality reads. This has not been a small or easy project, but we hope the improvements make the effort worthwhile as PeakTrace can now rescue many more marginal traces.

The full list of change include

  • New Feature. Support for ThermoFisher SeqStudio™ Sequencer.
  • New Feature. Fuse trace at base default is now 0.
  • Improved basecalling especially of low quality traces.
  • Improved trace processing.
  • Improved peak normalization.
  • Improved clean baseline.
  • Improved detection of PCR products.
  • Improved PeakTrace processing and basecalling through “dye blobs” peaks.
  • The signal start peak auto setting now sets the start peak to the value closest to the model expected value.
  • The automatic fuse trace at base or fuse basecalling at base on traces with large dye blobs peaks can be turned off by setting fuse basecall to -1.
  • Unit data and build date can be written to a text file with the -rf options.
  • Support temporary removed for the following machines and run types. These run conditions are rarely used, but support will be returned in the next major update.
    • ABI3700 runs
    • MegaBACE 1000 & 4000 runs
    • ABI 3130 80cm array runs
    • ABI 3730 runs below 6kV
    • The following ABI 310 runs
      • 36cm array runs
      • 50cm array runs
      • 30cm array runs with a voltage below 12 kV
    • All ET terminator runs
    • MJ Research Biostation runs
  • Update of the CodeMeter runtime to 6.60a. Due to limitations of the CodeMeter runtime support on Linux this update is only compatible with REHL7/CentOS7.
  • Many other bug fixes and internal improvements.

Auto PeakTrace 6.90 can be downloaded 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. The command line PeakTrace 6.90 version for Windows and Linux is also available on the PeakTrace:Box Downloads page.

This update is highly recommended for all users of the Auto PeakTrace or PeakTrace 6.82 and earlier.

Auto PeakTrace RP 6.90 Released

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Auto PeakTrace RP 6.90 Options

Auto PeakTrace RP 6.90 Options

We have released Auto PeakTrace RP 6.90. This is a very large upgrade and a significantly improved version of the PeakTrace Basecaller. We have spent the last 6 months optimising all the algorithms and code focused on improving the read length and appearance of poor quality traces. We will be writing about the many improved features over the coming weeks.

The full list of changes includes.

  • New Feature. Support for the ThermoFisher SeqStudio™ Sequencer.
  • New Feature. Fuse trace at base default now 0.
  • Improved basecalling especially of low quality traces.
  • Improved trace processing.
  • Improved peak normalization.
  • Improved clean baseline.
  • Improved detection and basecalling of PCR product traces.
  • Improved PeakTrace processing and basecalling through “dye blobs” peaks.
  • The signal start peak auto now sets the start peak to the value closest to the model expected value.
  • The automatic fuse trace at base or fuse basecalling at base on traces with large dye blobs peaks can be turned off by setting fuse basecall to -1.
  • An additional secondary PeakTrace RP server established in China.
  • Unit data and build date can be written to a text file with the -rf options.
  • Support temporary removed for the following machines and run types. These run conditions are rarely used, but support will be returned in the next major update.
    • ABI 3700 runs
    • MegaBACE 1000 & 4000 runs
    • ABI 3130 80cm array runs
    • ABI 3730 runs below 6kV
    • ABI 310 36cm & 50cm array runs
    • ABI 310 30cm array runs with a voltage below 12 kV
    • All ET terminator runs
    • MJ Research Biostation runs
  • Bug fix that prevented clear range trim from being applied to the front of the trace.
  • Many other bug fixes and internal improvements.

Auto PeakTrace RP 6.90 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. User of older versions should be notified by the automatic update feature.

This update is highly recommended for all users of the Auto PeakTrace RP or earlier.

An update for the standalone box versions of PeakTrace will be released in the next few days.