Bioinformatics for Beginners

Establishing and maintaining NGS data analysis software requires substantial expertise and effort that many forget to include in cost calculations. These costs are often significant and surpass the price of a software license or subscription.
High quality commercial software has teams of experts continually improving, testing, and updating pipelines for the most accurate analysis available. Additionally, commercially maintained software with clear documentation and access to a dedicated support team offers assistance when you need it most. Combined with features like a graphical user interface (GUI), these abstract away the complexities of bioinformatics so you can access consistent results quickly.

After libraries have been prepared and sequenced, Real-Time Analysis (RTA) software onboard the sequencing system provides base calls and associated quality scores.

Data coming off the sequencer is then processed through secondary analysis, where sequencing reads are aligned and assembled, to provide the full sequence for a sample and either provide DNA variant calls or RNA transcript counts.

The process of generating DNA variant calls typically reveals thousands to millions of variants, which are then interpreted in the final step of an NGS workflow, known as tertiary analysis, to derive biological insights. Tertiary analysis, or variant interpretation, enables users to ingest variant call files (VCF) and perform downstream analyses depending on the application, including gene expression/quantification profiles, heatmaps, visualizations for biomarker discovery, or single sample reports for research purposes

Data analysis costs may vary depending on the choice of software in addition to infrastructure and deployment options selected. For example, using open-source software often does not require a license or subscription, but may incur higher cost on computing, either on cloud or on-premises, and on resources associated with development and maintenance of pipelines. Commercial analysis software requires purchase of software licenses and/or subscriptions, often accompanied by higher accuracy, faster runtimes, reduced compute, and better support.
Illumina DRAGEN secondary analysis offers the most accurate and most comprehensive secondary analysis for Illumina sequencing data1. The analysis of each 30-35x human whole genome may typically cost $6-10 on the cloud (Illumina BaseSpace Sequence Hub or Illumina Connected Analytics) and could cost more in cases with compute-intensive pipeline configurations. The cost is approximately $1.5-2.5 for each human whole exome or transcriptome sample. For projects with a lot of data, DRAGEN ORA lossless compression (available on DRAGEN server and DRAGEN onboard instruments) can reduce cost of data transfer and storage costs by up to 80%¹.

For customers that choose to analyze and store their data in the cloud, Illumina offers clear and transparent access to account information to track and monitor compute and storage costs. For organizations that keep data stored over time, archiving data you don’t plan on accessing for many months or longer and deleting old data will also reduce the cost of data storage.

¹Data on file, Illumina Inc., 2024

A LIMS, or Laboratory Information Management System, is a tool used to effectively manage laboratory and sample data. For genomics labs, a genomics-specific LIMS is particularly important to manage the volume and complexity of sequencing data. The more samples your lab runs, the more important it is to use a genomics LIMS for accurate, efficient, and compliant wet lab data management. Implementing a LIMS can profoundly impact downstream analysis by enhancing data integrity through workflow standardization, automation, and accessibility. It helps laboratories maintain accurate records, streamline workflows, ensure quality control, and improve collaboration among teams.

Learn more about what a LIMS can do for your lab here.

Yes. Illumina offers a range of training options for customers. Once selecting the software solution best fit for your application areas and test menu, Illumina will scope your implementation and training needs. Integrated as part of Illumina’s software implementation packages, training is available to walk-through consulting, platform and filters set-up, data ingress set-up, project management, report customization, and other key software functionalities. Customers may also access the Illumina support site to learn best practices and latest techniques via online courses and instructor-led trainings.

Data security and privacy are essential components to consider before setting up your NGS experiment. Only you can know best whether to store your data locally or in the cloud; Wherever you choose, Illumina offers software with both deployment options available. Some factors to consider include if your region or organization has data storage requirements, or stringent compliance policies. If choosing to store your data locally, it’s important to consider how your organization will protect and secure the data. Depending on the size of your project and the volume of data, most organizations will find they need dedicated facilities and storage, which requires initial capital investment.

Storing data on enterprise clouds like Amazon Web Services (AWS) or Google Cloud Provider (GCP), provides access to a dedicated teams of cloud security and privacy experts to ensure that the data stored and accessed within the cloud environment are encrypted, private, and secure. With data already in the cloud, secure collaboration with colleagues is also streamlined.

For more information, visit Genomic Data Storage & Security.