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Nucleics

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 6.90 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.

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.

Auto PeakTrace RP 6.82 Released

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Auto PeakTrace RP 6.82 Options Window

Auto PeakTrace RP 6.82 Options Window

We have released an update for Auto PeakTrace RP (6.82). This is an intermediate release, mostly bug fixes and improvements, but it also has a couple of new features that are of interest for some of our customers. The full list of changes and improvements include:

  • New feature. Ultra-aggressive clean baseline cleaning when mixed peak threshold is set to 102.
  • New feature. Support added for:
    • ABI3730 ultra-rapid 50cm arrays runs
    • ABI3730 10.5kV50cm array runs
  • New Feature. European located secondary server ensuring data does not leave the EU.
  • New feature. Output both peaktrace processed and no peak resolution traces at the same time.
  • Improvement to basecalling include G-peak dropouts.
  • Bug fix that prevented the input and output folders being updated from the Auto PeakTrace RP 6 command line.
  • Improved basecalling and detection of low quality mixed peak traces.
  • Improved trace normalization.
  • Bug fix for trace trimming modules. On traces that are not improved, only soft trimming (abi limits) is applied. If the abi/kb basecaller is selected and set abi limit is unchecked then the trace will still be hard trimmed.
  • Version, build date are accessible from the Auto PeakTrace RP 6 command line.
  • Errors and processing progress when using Auto PeakTrace RP 6 from the command line are now output to the command line window.
  • Other bug fixes.

Auto PeakTrace RP 6.82 for Windows and (MacOS X will be released later) and can be downloaded from the PeakTrace RP downloads page. This release is also be available soon via the automatic update feature within Auto PeakTrace RP if you are using a recent version 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.

We will be releasing an update for the PeakTrace:Box version in the next few days.

Happy New Year 2018

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Everyone here at Nucleics is back at work after a relaxing few weeks enjoying the Australian summer and recharging after a hectic 2017.

Looking forward, we have many new updates and products coming out in 2018 that we are excited to share with our old and new customers. Watch this space!

Christmas and New Year Holidays 2017

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Life at Nucleics over Christmas

What a year 2017 has been! It is hard to believe it is almost at an end. All of us here at Nucleics are looking forward to a relaxing break over the Christmas/New Year period, lazying around in the summer heat and enjoying the food, sun and sand.

Nucleics will be closing on the 22nd December and will re-open on the 8th January. We will be keeping a lazy eye on emails over this time, but expect that our response rate might be a bit slower than usual.

We wish all our customers a Merry Christmas and Happy New Year and are look forward to helping you all in 2018.

Auto PeakTrace & PeakTrace 6.81 Released

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We have released a minor update for Auto PeakTrace and PeakTrace (6.81). The full list of changes and improvements include:

  • New Feature. Support added for
    • ABI 3730 ultra rapid 50cm arrays runs
    • ABI 3730 10.5kV 50cm array runs
  • Improved basecalling and detection of low quality mixed peak traces.
  • Improved trace normalization.
  • Bug fix for trace trimming modules.
  • With traces that are not improved, only soft trimming (abi limits) is applied. If the abi/kb basecaller is selected and set abi limits is unchecked then then the trace will still be hard trimmed.
  • Other bug fixes.

Auto PeakTrace 6.81 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 6.81 for Windows and Linux is also available on the update pages.

This update is an optional update for all users of the Auto PeakTrace or PeakTrace 6.80. For user of Auto PeakTrace the changes are automatically applied on the server end.

Auto PeakTrace 6.63 & PeakTrace 6.63 Released

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Auto PeakTrace 6.63 Options

Auto PeakTrace 6.63 Options

We have released a bug fix update for Auto PeakTrace and PeakTrace (6.63). The full list of changes and improvements 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 when using hard trim.

Auto PeakTrace 6.63 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 recommended update for all current users of the PeakTrace:Box System.

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.