The GenNext platform has many analysis workflows for processing next-generation sequencing (NGS) raw data. Within the scope of DNA sequencing, it is possible to analyze germline clinical exome (CES), whole exome (WES), whole genome, and somatic targeted, whole exome, whole genome sequencing data. In addition, GenNext provides customized analysis flows for the processing of RNA sequencing data. GenNext, apart from any other platform currently available, also offers the option to analyze DNA and RNA sequencing data simultaneously.

GATK-best-practices workflow is followed in the analysis workflows used for data processing within the GenNext_klinik platform. In this context, in the standard workflow where the raw data is uploaded to the platform for analysis, the process starts with the quality control of the data, and the variant file is obtained after the standard NGS data analysis steps (https://gatk.broadinstitute.org/hc/en-us/articles/360035894711-About-the-GATK-Best-Practices). Depending on the format of the uploaded file, GenNext_klinik starts the analysis workflow at the appropriate step. In addition to the standard analysis workflow, GenNext_klinik is flexible enough to add extra steps according to user demand. You can contact our team to discuss the details of customized analysis workflows, and you can find the details of the analysis tools and algorithms used within the platform in the relevant document (PIPELINEs, ANALYSIS DOCUMENT LINK).

The GenNext_klinik platform uses a GPU-powered data processing infrastructure. Thanks to this infrastructure, human WGS data with 30X coverage is processed in 15 minutes and 90 minutes on our fastest and slowest nodes, respectively.

The variation in the data processing and analysis speed of the GenNext_klinik platform is one of the problems that GenNextCloud service users may encounter. GenNextCloud servers are GPU servers located in Türkiye and have an upload/download speed of 10 Gb. Therefore, since even a slight change in your connection speed may also affect your upload speed, you may observe that file upload and analysis processes take longer. In non-GenNextCloud services, connection problems are unlikely to occur as the compute engines are located at the user premises.

In addition to processing sequencing data with the GenNext_klinik platform, variant analysis can also be performed from VCF files. In addition to a variety of variant analysis tools and approaches that you can customize for your case, GenNext_klinik also offers GenNext-Best-Practice filtering options for the convenience of its users. Detailed information about GenNext_klinik’s options for variant analysis and GenNext-Best-Practice can be found in the related document (GenNext-Variant Analysis document- LINK).

GenNext_klinik offers filtering options for solo analysis as well as duo and trio case analyses. After the user assigns the data with Sample IDs of the individuals to be analyzed to the “Filter” field before the analysis, GenNext_klinik lists the variants that meet the criteria, again, defined by the user. The user can also use GenNext-Best-Practice filtering options for these analyses (GenNext-Variant Analysis document- LINK).

GenNext_klinik offers an export option for the variant list after analysis. You can export the variant list as a TSV file by simply clicking the “Export” button that you can access from the GenNext-Variant tab where you performed the analysis.

GenNext offers various filtering options to the user before variant analysis. In this section, the user can upload a pre-prepared gene list by themselves to the system or use the gene list creation option provided by GenNext_klinik. In this context, when the user adds the phenotypic features of the case in the format of Human Phenotype Ontology (HPO) terms, it becomes possible to create a list of the genes that are associated with the phenotype according to the HPO system. The gene list is expanded for each term added. In variant analysis with the gene list, please be aware that only the variants located in the genes provided in the list will be displayed.

GenNext_klinik uses multiple variant callers (HaplotypeCaller, DeepVariant, FreeBayes, BCFTools) within the analysis workflow and generates separate VCF files from each. It is up to the user to decide which variant callers to include in the workflow before the analysis. Unless the user makes a choice, GenNe GenNext_klinik uses DeepVariant as the default variant caller (for more information on variant callers, see GenNext-Variant Analysis: GenNext-Variant Analysis document- LINK).

The GenNext_klinik platform has the capacity to analyze multiple data simultaneously. In this context, when the user is uploading files, GenNext_klinik offers the option to upload files in a “batch“. This allows the user to transfer multiple files to the platform in a single upload step. After the platform detects that multiple data files are uploaded, the user is also given the opportunity to perform a “joint-call” for the uploaded data. If “joint-call” is not selected, each data is transferred to the relevant analysis workflow and processed separately to create the VCF files. With the “joint-call” option selected, the uploaded data is combined into a single VCF file at the end of the analysis workflow. Since multiple file uploads require large data transfers, they can only be performed with GenNext Compute Engines (GCEs) (see relevant document LINK).

Within the GenNext_klinik platform, the user is offered ten report draft options. The user can choose any of the drafts they deem appropriate for reporting. At the same time, the user can automate variant reporting by adding their own designed report format to the system. For the creation of user-specific report formats, please contact our team.

To get the variant result report, click on the “Report” button after selecting the relevant variant. The information entered by the user on the GenNext_klinik platform (Sample ID, Analyst, Physician, etc.) is used to fill in the relevant fields in the report. The generated variant reports are listed in the “Reports” field on the left menu and can be downloaded in PDF format.