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Nucleics

Sanger DNA sequencing basecalling for improved read quality and accuracy.

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Overview

Nucleics is a software company specialising in DNA sequencing tools, primarily focused on improving the quality and output of Sanger sequencing data. The company develops basecalling software and related utilities that process raw sequencing trace files to produce more accurate and higher-yield sequence reads. Nucleics serves DNA sequencing laboratories and facilities that rely on Sanger sequencing workflows.

Core Products

  • PeakTrace Basecaller: A Sanger sequencing basecaller that can deliver up to 50% more high-quality bases compared to standard basecalling approaches. Available for Windows and Linux platforms.
  • PeakTrace:Box: An onsite hardware and software basecalling system designed to improve Sanger DNA sequencing traces within a laboratory's own infrastructure.
  • Auto PeakTrace RP: An online version of the PeakTrace Basecaller that provides full control over basecalling settings, allowing users to configure and run basecalling remotely.
  • QualTrace / QualTrace III: Additional DNA software tools offered alongside PeakTrace, available for purchase as units or software licenses.

Licensing and Deployment

  • PeakTrace is licensed via a USB key system that contains an independent clock, which must be kept in alignment with the host computer's system time.
  • License updates are distributed by email and applied to the USB key through an update file installation process.
  • The CodeMeter Runtime is required for running Auto PeakTrace 6, and users upgrading from earlier versions must update this runtime as part of the upgrade process.
  • PeakTrace:Box customers have access to dedicated download pages for the latest software updates.

File Format and Technical Capabilities

  • PeakTrace processes .ab1 input files, which are the standard trace file format produced by Sanger sequencing instruments.
  • Version 6.96 introduced support for generating PHRED .poly file output, where each output file takes the name of the corresponding input .ab1 file and includes a structured header line.
  • Auto PeakTrace RP 6.96 added support for additional run conditions and expanded .poly file output support.

Recent Software Releases

  • Auto PeakTrace 6.961 and Auto PeakTrace RP 6.961 (June 2023): Minor bug fix releases addressing an issue with the archive function. The bug did not affect command-line versions of PeakTrace.
  • Auto PeakTrace 6.96 and PeakTrace 6.96 (May 2023): A major release recommended for all users of version 6.952 or earlier, incorporating improvements, updates, and bug fixes across Windows and Linux builds.
  • Auto PeakTrace RP 6.96 (May 2023): A Windows update incorporating a large number of changes and enhancements, including new .poly file output support and expanded run condition support.

Pricing

  • PeakTrace, PeakTrace RP, and QualTrace are available for direct purchase through the Nucleics website.
  • In June 2023, Nucleics increased prices for these products by 20%, the first price change since 2015, citing a high-inflation environment as the reason for the adjustment.

Nucleics maintains an active support and news blog covering software release notes, upgrade guides, licensing procedures, and operational notices, providing documentation resources for existing users managing PeakTrace deployments.