Nucleics

Nucleics

Auto PeakTrace & Auto PeakTrace RP 5.51 Update Released

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We have released a small update for both Auto PeakTrace and Auto PeakTrace RP (5.51). This version just fixes a small bug with the use of a particular option set. We have also released new automatic updates for both these versions so if you are running an older version of these programs then you should be prompted to install the update at some point over the next week or so.

Auto PeakTrace 5.50 Released

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A major update to Auto PeakTrace has been released. There will be updates released shortly for Auto PeakTrace RP and the Linux version of PeakTrace.

This update can be obtained from our downloads page. Please contact us for access to the downloads page if you do not have the password.

The complete list of changes are

  • New Feature. A nolog option to suppress output of the PeakTrace logfile (comand line only).
  • Improved fuse basecalling option.
  • Improved basecalling through large dye peaks.
  • Default options changed to improve basic usage
    •  .seq file output: abi
    • required good base improvement: -20
    • q average trim: Q12 average in 20 base window
    • n base threshold: 5
    • skip short traces: yes
  • A short trace is now considered to be a trace with fewer than 500 bases.
  • Improved support for ET terminator traces.
  • Improved support for ABI3500 BigDye 1.1 traces.
  • New error code 36 added – Input and output paths are the same.
  • New error code 38 added – Skipped short trace.
  • Good quality threshold and N base threshold now have maximum values of 99.
  • The usual bug fixes and tweaks.

Publications mentioning the use of PeakTrace

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I thought I would start posting papers that have mention that they have used PeakTrace. Here is the first of these posts — Phylogenetic Relationships of Muehlenbeckia, Fallopia, and Reynoutria (Polygonaceae) Investigated with Chloroplast and Nuclear Sequence Data published in International Journal of Plant Sciences, Vol. 172, No. 8. (October 2011), pp. 1053-1066. The authors of this paper claimed they were able to get 300 extra bases out of their reads using PeakTrace.

Changes to PeakTrace Online

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PeakTrace Online (the free version of PeakTrace) has always used a very basic group of settings. One area that can cause it problems are traces with weak signal at the end of the trace. This is because PeakTrace Online was using any of the trace trim settings. While it should not really matter, some people get worried when seeing a large number of low quality base calls at the end of the trace. Personally I would rather have a low quality call rather than no call at all, but many people prefer these low quality regions removed.

To avoid this I have changed the online settings so that PeakTrace now uses the window quality score trimming options. PeakTrace Online will now trim any region where the average quality score in a 20 base window drops below 12 (i.e. -wq 12 20).

Auto PeakTrace 5.40 released

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A major update has been released for Auto PeakTrace (5.40). This release provides support of Unicode characters in file paths. This change involved making over 3000 code changes so we are not pushing it out as automatic update yet, but if you want to try it you are welcome to contact us to obtain the new version.

The change log for this release:

  • New Feature. Unicode path support.
  • New feature. Unicode logfile output.
  • New Feature. Post-processing trace trimming without re-processing.
  • Auto PeakTrace checks the CodeMeter runtime version installed and prompts if an update is needed.
  • Auto PeakTrace checks if the CPU supports SSE3 instructions.
  • CodeMeter runtime is no longer included with the Auto PeakTrace installer.
  • UI improvements
  • Most likely some new bugs introduced due the large number of changes needed to support Unicode paths

Auto PeakTrace 5.11 Released

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A major update to Auto PeakTrace software incorporating an improved fuse basecall setting and the new no peak resolution option. The update should be automatically updated by user using Auto PeakTrace 5.05 for systems that are online. For users that run the PeakTrace:Box system offline please contact Nucleics to obtain the update.

PeakTrace 5 Released

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PeakTrace 5 is the latest version of the PeakTrace basecalling software. This release offers a new licensing system, improved basecalling, automatic checking for updates, and an improved help manual. If you are an existing customer and wish to update to PeakTrace 5 please contact us.

PeakTrace 4.96 Released

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An update to PeakTrace software offering improved basecalling and trace processing. If you are an existing customer and wish to upgrade to version 4.96 please contact us.

PeakTrace Basecaller Released

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We have released a new DNA sequencing basecaller called PeakTrace designed to improve the read length obtain from all ABI DNA sequencers. This software can improve trace read lengths by up to 100% and is compatible with the ABI377, ABI3700, ABI310, ABI3100, ABI3130, and ABI3730. We have also made available a free version of PeakTrace basecaller to allow potential customers to try PeakTrace on their own traces.