BaseSpace Hub NGS Data Analysis (2024)

FAQs

How do you analyze NGS data? ›

The key steps for NGS data analysis are cleaning, data exploration, visualization, and deepening. Whether you perform genomic, gene expression, or methylation analyses, you can apply these steps in this article and some valuable tools to help you process high-throughput data.

After logging in to your BaseSpace account, select the RUNS tab at the top of the page. Select the blue hyperlink of the run you wish to requeue. Select the hourglass symbol drop-down menu, then select Requeue and then Sample Sheet. Note: this option will be grayed out if you are not the owner of the run.

Hardware Requirements

Memory: At least 16 GB of RAM is the minimum, but 96+ GB is ideal for handling large datasets. Disk Space: You need at least 500 GB of disk space, but 10+ TB is ideal for storing extensive data. CPU: A quad-core Intel Xeon CPU at 3GHz or higher is recommended.

Next-generation sequencing workflows start with nucleic acid isolation, followed by library preparation. Libraries are sequenced on Illumina sequencing systems, designed to support a wide range of applications and throughputs. Data generated are then analyzed to gain insights.

The NGS data analysis process includes three main steps: primary, secondary, and tertiary data analysis. Some steps are performed automatically on the sequencing instrument, while other steps occur after sequencing is completed.

Quality control metrics

Read analysis: Read length, GC content, adapter content and duplication can be measured to give an indication of data quality. Q score: A score that determines the probability that an incorrect base was called during the run. This is determined by Q = –10 log₁₀ P.

Navigate to the Runs or Projects tab list on BaseSpace. Select the check box next to Run Name or Project Name to be shared. Select the "Get Link" option, and Activate a link for the Run/Project. Copy the link and send it to the appropriate recipient(s).

What are the 4 steps of NGS? ›

Next generation sequencing (NGS) encompasses several technologies and techniques that enable high-throughput sequence analysis. It provides both qualitative and quantitative data, combining the advantages of qPCR and Sanger sequencing.

NGS is complex testing

Physicians and patients deserve to get the results of a next-gen sequencing test with the shortest possible turnaround time (TAT). Average laboratory TAT is 14-28 days.

NGS enables the interrogation of hundreds to thousands of genes at one time in multiple samples, as well as discovery and analysis of different types of genomic features in a single sequencing run, from single nucleotide variants (SNVs), to copy number and structural variants, and even RNA fusions.

By using multiple QC tools, following standard protocols, and using high-quality references and standardized annotation, researchers can ensure that their NGS data is of high quality and can be used for downstream analyses. All of the aforementioned tools are available through the Basepair platform.

A concise and straightforward NGS report contains details of the tumor sample, the technology used and highlights not only the most important and potentially actionable results, but also other pathogenic alterations detected. Variants of unknown significance should also be listed.

A common approach to interpreting gene expression data is gene set enrichment analysis based on the functional annotation of the differentially expressed genes (Figure 13). This is useful for finding out if the differentially expressed genes are associated with a certain biological process or molecular function.

The bases are read in order from left to right and top to bottom (on a chromatogram having more than one row of information). This order corresponds to the 5' end of the sequenced DNA to the 3' end. Such evenly-spaced, clear peaks make base calling straightforward and unambiguous.