omnomicsQ Validation calculates quality metrics for raw sequence (gzipped .fastq), for aligned reads (.bam), and for the validation the list of variants is required in vcf format. The bed file is required to define your region of interest.

omnomicsQ Validation is accessed with a web browser.

When you login to the server, you have access to the validation module on your laboratory space. At the beginning of the validation procedure you are requested to select your reference standard and provide information about your procedure. Thereafter, the system will perform the concordance analysis and compute the critical parameters as well as create the full table of concordance between your called variants and the expected variants. The system uses the bed file you submit to define your region of interest and finds its intersection with the truth set.

omnomicsQ gives you the facts about your data. Validation is a good starting point. The best way to experience more features is to register for a trial period.

Once you start to accumulate data in your database, you will be able to compare. Comparisons can be done in many ways: follow quality over time for a given procedure, compare procedures, validate a new procedure, compare kits, sequencers and find dependencies between parameters that can help you save time and costs, compare to industry standards or to peers.

Procedure accreditation usually requires quality metrics data to be stored so that an assessment can take place at any moment. Your omnomicsQ database provides transparency and an audit trail.

The Validation module requires human intervention and is not meant to be integrated into a computational pipeline. The vcf, and bed files to be used for validation are uploaded to a server.

The other parts of omnomicsQ QC software – not the Validation – whether integrated or operated from the graphical user interface, run locally. Therefore, no sample data is transferred beyond the security limits of the laboratory. The QC data for the files is uploaded to a server. For integration of the QC module see sample QC.

The list of available reference standard truth sets is open. Presently we have truth sets from NIST/Genome in a Bottle (NA12878_HG001, NA24385_HG002, NA24149_HG003, NA24143_HG004, NA24631_HG005), as well as some cancer cell lines (CCRF-CEM, HCT-15, HT-29) about which more information is available at several places on Internet, including ATCC: The Global Bioresource Center and Catalogue of somatic mutations in cancer.

We can integrate user truth sets (provided as vcf files to our customer support). Users of commercial reference standards by Horizon Discovery, such as the OncoSpan reference standard, can access our software also on our partner’s site (OncoMatic).