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CIDR-Authored Software Applications


The CIDR software development team creates analytical, bioinformatics, laboratory information management and utility applications that are tightly coupled and integrated with our custom databases. A small subset set of these applications amenable to de-localization have been prepared for external distribution as open source applications and are available at Bitbucket now. More CIDR applications will be added as time permits.


AutoCall Pipeline and Genotyping Data Release Tools

Since 2006, genotype calling and QC have been performed by several iterations of AutoCall, a Java application integrated with the CIDR WebLIMS and Phoenix sample handling system. AutoCall is an automated analysis pipeline for data generated by Illumina's Infinium genotyping products. CIDR’s pipeline augments the functionality of Illumina®'s "AutoConvert" utility, which converts scanner-produced IDAT files into GTC files. These GTC files are then read to calculate metrics from these data, including call rate, AA/AB/BB call frequencies, mean intensities for raw X and raw Y, estimated gender, and no-call and total call counts. Starting in 2015, these GTC files are also used to generate release genotype files and PLINK files via a set of Genotyping Data Release Tools mirroring some of the functionality of Illumina’s GenomeStudio, but designed to more smoothly handle very large genotyping projects. Autocall is currently being reworked to allow closer integration with the Genotyping Data Release Tools, and to take better advantage of a new set of GTC parsing and analysis utilities written in 2014.


Bioinformatics Applications Manager (BAM)

CIDR staff typically access our information systems through Web or Java client-based graphical user interfaces created by the CIDR software development team. Most CIDR custom software is executed via the Bioinformatics Applications Manager (BAM). Written in-house using Java SE 7 and JavaFX, the BAM provides a single consistent desktop GUI for most applications, regardless of programming language or other constraints.



Our CIDRSeqSuite sequencing data analysis pipeline was developed to automate a variety of next-generation sequencing analyses. It runs on 64-bit Linux and is written in Java SE 7. The current version of CIDRSeqSuite focuses on individual tasks and the interdependencies among them. When an analysis is submitted to the CIDRSeqSuite server, all required tasks and their interdependencies are stored in a relational database. Such tasks include alignment, variant annotation, and even the demultiplexing of an individual tile from a flowcell lane. Tasks are submitted by the server process to an SGE-enabled cluster. As each task finishes, its status is stored in the database; any tasks whose dependencies are complete are then submitted. A retry policy resubmits failed tasks. Email notifications are sent upon the completion of analyses and when errors such as repeated task failures occur. Tasks can be submitted to the compute cluster via command-line tools or a graphical user interface. CIDRSeqSuite includes integration with Bina RAVE deployed on a single Bina Rack local analysis appliance as well as a CIDR-authored highly parallel BCL-to-FASTQ de-multiplexer.


CIDR WebLIMS Infinium Chemistry

To handle the workflow complexity and volume of data for large-scale GWAS genotyping projects, CIDR developed a system for sample tracking and quality control customized to our high-throughput environment and need for flexibility. Written in Java and JavaScript with a MySQL back end, the WebLIMS tracks each sample through all stages of processing by recording all variables essential to quality control, with integrated data validation to reduce errors. The WebLIMS has been in daily production use since 2006, with major changes in 2014.



CidrDB is a Java framework for managing MySQL database connections. It is open source code, publicly available on CIDR's public Bitbucket repository.



A collection of Java utilities for file parsing, text manipulation, GUI design, and more, also open source, can be downloaded from Bitbucket.



Phoenix is a sample tracking system developed in-house by the CIDR software development team. Designed to accommodate the volume and complexity of sample management for CIDR’s SNP genotyping and next-generation sequencing work, Phoenix has been used in production starting in 2015. Now in the last stages of development is a web portal that will allow investigators to communicate with Phoenix to upload files, check on the progress of their projects, and respond to problem reports. Phoenix provides the flexibility and sophisticated problem-handling that enables us to deliver the high-throughput, high-quality service that makes CIDR a unique national resource to the life science research community. Current work includes integrating project management features.


SRA Submission Tool

Now on available for download on CIDR's public Bitbucket repository ( is an automated tool for packaging and submitting raw sequence data to the Sequence Read Archive (









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Software Developers Alice Sanchez, Sean Griffith, Ben Myers, Kevin Duerr.