Kaleidaseq

Software for Monitoring Data and Projects  in Sequencing

• Kaleidaseq - Version 0.3

  Download    Demo   Architecture README  Article

  Kaleidaseq tracks sample and projects in shotgun sequencing. It can be used to monitor process queues, base-call samples, extract and store the read length statistics in a relational database, transfer files to appropriate directories and browse the sequencing performance through the web. Sample-sheets for gel loading can be created through a web interface.

  Kaleidaseq is written in Perl, has been tested on UNIX and utilizes the mysql relational database. The web application and a accompanying UNIX script have been used successfully in a demanding production environment at CSHL's Genome Center for about 2 years. The database has successfully handled the entry of about 300,000 samples. The schema is covers the production phase of large-scale sequencing comprehensively.

  Kaleidaseq is designed to be modular and extensible. New steps and new tracking variables can be added easily. Using the base architecture and the core libraries a programmer can develop new workflow applications.

  New in Version 0.3

  Version 0.02 had the functionality of monitoring the process queues and creating sample sheets. Version 0.3 has the following new features:

  • A new script APP that runs on the UNIX command-line can base-call traces using phred, extract read length statistics, store the statistics in a relational database and transfer files to project directories. App also sports a graphical interface which can be used by finishers. Customization is possible with the help of a configuration file.
  • The web interface of Kaleidaseq can be used to browse the sequencing statistics stored by APP. You can start from a page that shows the number of reads, success percentage and mean read length for the last 7 days and each day in the last 7 days. This page also breaks down the statistics by division, reaction chemistry, team and machine. You can then traverse links that take you from gels and plates processed in the last week to viewing the samples from a single gel to viewing a single trace.
  • Extensive configuration of APP and Kaleidaseq is possible.

  Files in Kaleidaseq

  • README  - instructions for installation and a short tutorial.
  • kaleidaseq.cgi    - the main CGI script.
  • kaleidaseq.cf      - configuration file to set the modules and database schema.
  • sequencing_constants.cf  - configuration file to set  up and customize web interface of Kaleidaseq and APP.
  • schema   - the complete database mysql database shema.
  • Bio::Unit.pm - library module that models process queues and allows for rapid creation of web-based workflow applications.
  • Bio::ProductionSequencing.pm - library module used by APP and web interface of Kaleidaseq to base-call traces, extract and store statistics, transfer files and create text and HTML reports.
  • Bio::AlphaNumerals.pm - library module to create alphanumerical series.
  • templates/Home.tem - template file for the home page of Kaleidaseq. The following files are template files for the appropriate module.
  • templates/ProjectRegistry.tem
  • templates/PlaqueBoxes.tem - tempate file fo
  • templates/TemplatedPlates.tem
  • templates/ReactedPlates.tem
  • templates/Gels.tem