Kraken laboratory workflow management software

Kraken™ software is a complete LIMS platform that handles all laboratory processes including sample management and tracking, data analysis and reporting.

Our proprietary Kraken™ software is a dedicated information and laboratory workflow manager. Kraken workflow manages the time consuming and error prone data handling and planning associated with DNA extraction, genotyping and DNA sequencing. This system was developed by scientists for scientists, and we use Kraken on a daily basis to run all of our genomic service projects in Europe and the USA.

Every project is given a unique project number, and all associated sample plates, KASP assays, and genotyping results are tracked within the project. 

Key components of the Kraken software

  • Project management module
  • Sample management and tracking module
  • Meridian3 engine control interface for dispensing
  • Genotyping data analysis and reporting module (this component of Kraken is also sold separately as KlusterCaller™)


  • Multiple graphic user interface to shared database
  • Password-protected multi-level secure data storage
  • Multiple projects can be run simultaneously and are viewed by customer and project
  • Complete user tracking to event log file
  • Automatic job report details work schedules
  • Barcode tracking of plates and tubes - fully searchable
  • Large scale project capability with super fast access powered by MySQL
  • Strict operating option ensures users log freezer and plate storage locations.

DNA sample management

  • Master DNA layout graphical organiser
  • Plate layout importer
  • Plate replication tracking 96 - 384 - 1536 - any user definable format
  • Assay + sample plate tracking
  • Freezer storage tracking
  • Robotic interface utilities for fully automatic plate tracking (DLLs and command line programs)
  • Thermal cycle parameter tracking
  • Genotyping features

Reading and calling

  • Direct plate reader import – ABI (txt + sds), PerkinElmer, Tecan, Labsystems, BMG
  • Storage of multiple reads of the same plate
  • Automated/manual cluster calling for plate reader files
  • Compare differences between calls on plates
  • Plate reader compensation factors may be applied
  • Multiple assays can exist on the same plate
  • Multiple master plates may be viewed individually as clusters
  • Hardy-Weinberg analysis.


  • Definable export report
  • License free read-only cluster viewer software compatible
  • Ability to check for duplicates
  • Ability to drill down to identify bad samples.

Sequence features

  • Sequence primer storage and management
  • Primer to DNA sample tracking
  • ABI sample sheet generator (User definable for other manufacturers)
  • Embedded viewer enabling multiple traces to be displayed and scored
  • Data exporter and report generator.


The Kraken manual is available here.

If you are using Kraken in your laboratory and have a new support issue, please email

We are continually improving Kraken to meet the needs of our customers.  One year of free Kraken updates are included in the cost of a Kraken purchase.