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In depth look at the features of PeakTrace 6

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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 have created a series of posts looking in depth at what these new options do, how they can best be used, and how they can help our customers make the most of PeakTrace.

Auto PeakTrace 6.96 Options

Auto PeakTrace 6.96 Options

The PeakTrace options covered in depth include:

Auto PeakTrace RP 6.94 Released

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Auto PeakTrace RP 6.94

Auto PeakTrace RP 6.94

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
  • 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.

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 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 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.

Auto PeakTrace RP 6.80 Released

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Auto PeakTrace RP 6.80 Options Window

Auto PeakTrace RP 6.80 Options Window

We have released an major feature release for Auto PeakTrace RP (6.80). The full list of changes and improvements include:

  • New Feature. Total traces processed and success rate shown.
  • New Feature. Auto PeakTrace RP 6 can be used as a command line program.
  • Improvements to fuse basecall and fuse trace with difficult sequences.
  • Improvement of the basecalling of “drop out” peaks.
  • Improvements to extra normalization of PCR product traces.
  • More accurate estimated time for trace processing completion.
  • Other bug fixes and enhancements.

The major change of this release is that Auto PeakTrace RP 6.80 can now be used from the command line. This allows the easy integration of Auto PeakTrace RP 6.80 into various LIMS scripts.

If Auto PeakTrace RP 6.80 is used from the command line with no options it will use the settings (including the input and output directories) saved from the last use of Auto PeakTrace RP 6. The saved settings can be overwritten by the use of command line switches. If no switch value is provided on the command line then value in the save setting file will be used. Settings that are changed via the command line update the setting file for future runs of Auto PeakTrace RP 6.

It is recommend that if you wish to use Auto PeakTrace RP 6 in a command line script that you first contact Nucleics @ {This email is obscured. Your must have javascript enabled to see it} or your local supplier for advice.

Auto PeakTrace RP 6.70 for Windows and (MacOS X will be released later) and can be downloaded from the PeakTrace RP downloads page. This release is also available via the automatic update feature within Auto PeakTrace RP if you are currently using a recent version.

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 RP 6.70 Released

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Auto PeakTrace 6.70 Options Window

Auto PeakTrace 6.70 Options Window

We have released Auto PeakTrace RP 6.70. This update improves the processing and basecalling of .ab1 trace files. The full list of changes include

  • Improved support for NanoPOP™-7 polymer and BrilliantDye™1.1 chemistry traces.
  • Force processing makes PeakTrace basecall the low quality data regions.
  • Improved support for more non-standard run conditions and voltages.
  • Improved basecalling.
  • Improved mixed basecalling.
  • Bug fixes and enhancements of trace processing.

Auto PeakTrace RP 6.70 for Windows and MacOS X can be downloaded from the PeakTrace RP downloads page. This release is also available via the automatic update feature within Auto PeakTrace RP if you are currently using a recent version.

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. We will be releasing an update for Auto PeakTrace (Box version) in the coming days.

Auto PeakTrace RP 6.63 Released

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Auto PeakTrace RP 6.63 Options

Auto PeakTrace RP 6.63 Options

We have released Auto PeakTrace RP 6.63. This update fixes a number of bugs and improves the processing of .ab1 trace files under certain run conditions and PeakTrace settings. The full list of changes include

  • Improved clean baseline and extra baseline modules.
  • Improved comparison between KB and PeakTrace basecalls.
  • Improved processing of low resolution traces.
  • Improved mixed basecalling.
  • Bug fix for picket fence output.
  • Bug fix preventing reltrace output with hard trim.
  • Improved skipping of low quality mixed traces.
  • Improved support for BrilliantDye traces for the ABI 3730 instrument with the 50cm array.
  • Bug fix to prevent output of zero length .seq files when skip short traces checked, no trimming used, and set abi limits checked.

Auto PeakTrace RP 6.63 for Windows and MacOS X can be downloaded from the PeakTrace RP downloads page. This release is also available via the automatic update feature within Auto PeakTrace RP if you are currently using a recent version.

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 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 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.