NGS – Console Scientific PipelinesNGS Pipeline is dedicated for laboratories running next generation sequencings tests. It integrates various tools and packages including GATK, Picard, SAMTools, FASTQC into one simple and ease to operate automated framework. The modular architecture of the pipeline enables incorporating alternative open-source and commercially available bioinformatics packages and algorithms. Each step of your pipeline can be overlooked in a real-time manner providing full control of the process. In addition to that, users have an access to variety of output files, including BAM file, BAI file, VCF file and final CVS report. Using data included in InterOp and FASTQ files you can visualize run and sample QC parameters and set customizable thresholds with different restriction levels easing the decision to proceed with the pipelines. QC can be controlled on both run and sample level by changing distinct sequencing parameters. NGS Pipeline is ideal for customers working with large datasets demanding paralleling of analysis to shorten time from sample collection to final report generation. Depending on the requirements of laboratory, various sequencing protocols can be analyzed, including whole genome sequencing (WGS), whole exome sequencing (WES), Trio analysis and customized panels. A key application of NGS Pipeline is detection of genetic variants associated with disease phenotypes. Detected variants can be filtered using curated disease-associated gen sets but also by applying personalized filters based on patients’ phenotype.  A review of bioinformatic pipeline frameworks” Briefings in bioinformatics vol. 18,3 (2016): 530-536.
QC & Control
With data included in your InterOp and FASTQ files you can visualize your run and sample QC parameters and set customizable thresholds with different restriction levels easing the decision to proceed with your pipelines. QC can be controlled on both run and sample level by changing distinct parameters like: Per base sequence quality, Per tile sequence quality, Per sequence quality scores, Per base sequence content, Per sequence GC content Per base N content, Sequence Length Distribution, Sequence Duplication Levels, Overrepresented sequences, Adapter Content.
Insight into entire pipeline process
Each step of your pipeline can be overlooked in a real-time manner to make sure you can control the process. In addition to that, you will have an access to variety of output files, including BAM file, BAI file, VCF file and final CVS report.
Understanding the necessity to process your data swiftly and efficiently NGS Console uses paralleling algorithms to enable the run of few pipelines at the same time.
Prioritizing your pipelines is a key to successfully conduct outcomes and release reports when you are dealing with changing and dynamic clinical situations. NGS Console enables to manage the order of running your pipelines and prioritize samples based on current necessities.
Full range of DNA sequencing analysis
Depending on the requirements of your laboratory, you can analyze outcomes of various sequencing protocols, including whole genome sequencing (WGS), whole exome sequencing (WES), Trio analysis and customized panels.
NGS Console can be fully integrated with our LIMS system. Which allows you easily manage all of your tests in LabStorm and transfer orders directly to Console.