Next generation sequencing (NGS) technologies have revolutionized genomics and metagenomics. NGS is a high-throughput technique that can potentially sequence large volumes of DNA fragments simultaneously. Its low running cost and high speed have made NGS the go-to sequencing method for most clinical studies and research.

What is the challenge of NGS data analysis?

The presence of automated software for NGS sequence analysis has made the job easier for the researchers. Now, they don't have to manually align and compare the sequences to the already established genome libraries. Since the NGS data is always large, heterogeneous, error-prone, and sparse, the presence of standardized NGS data analysis software can help in optimal alignment and analysis of the DNA seq data within a short period. 

In the last decade, quite a few analysis tools and software platforms have emerged with the promise of simplifying NGS data analysis. However, most of them share two common traits:

  1. Their evolution lags behind data generation capabilities of NGS 

  2. There is a gap between the format in which the analyses are delivered by the software and the format expected by the end-user

The gradual evolution of the NGS data analysis software platforms is showing the hope of bridging the gap between the developer and the user. Moreover, the ease of access promises the integration of the NGS analysis software applications in routine healthcare at the point-of-service level. 

What are the integral steps of NGS data analysis?

Nonetheless, the plethora of NGS data analysis software platforms now available does make the work of researchers and clinicians easier. NGS data analysis can be applicable for whole genome sequencing, whole exome sequencing, targeted gene sequencing and creating updated DNA archives on existing databases. Apart from DNA sequencing, NGS technologies can be applied for RNA sequencing, learning about gene expression profiles, and exploring protein-DNA interactions. 

NGS data analysis refers to the complete process of DNA sequencing analysis that includes multiple steps. All steps are part of the automated analysis set up run by the NGS data analysis software. The typical DNA seq analysis consists of the following steps – 

1. Primary data analysis

    The real-time analysis of the DNA sequences is completed during the first few runs of sequencing and imaging. Depending on the software platform you choose, you will receive base calls and/or quality scores at this point in the analysis. These scores will determine the primary structure of DNA. The NGS data analysis software will also perform the primary data analysis at this step automatically. 

2. Secondary data analysis

    Basepair NGS data analysis software offers one-click DNA sequence alignment and variant calling options. You can also explore different data visualization options during this step. 

    The assembly and analysis will provide you with the full sequence of the DNA sample. It should aide in the determination of genetic variants.

3. Tertiary data analysis

    The interpretation of genetic variation can shed new light on genetic diseases. Clinical studies and researchers can now venture into the depths of pathogenesis, disease progression, prognosis, treatment efficiency, personalized treatment/therapy, and predict the outcome within a couple of hours only. 

Why do researchers need automated NGS data analysis software?

The scores of NGS data analysis software now available in the market demand no expertise in coding or programming language. It is easy to operate these sets of tools and make minute changes to reset the parameters of your experience. The learning curve is almost linear since many of them work optimally irrespective of DNA sequencing platform.

The presence of automated NGS data analysis software platforms with easy user interfaces eliminates the need for learning complicated software commands and coding. It provides transparent and easily scalable options for the determination of DNA sequences and quality analysis. They offer the end-users interoperable software interfaces along with intuitive user interfaces on multiple devices. The availability of standardized NGS pipelines makes it easier for researchers and their teams to get their hands on publication-ready report formats within a couple of hours, if not less.

What aide can you expect from a good NGS data analysis software?

A good, state-of-the-art NGS data analysis software always helps with the analysis of DNA sequencing data in the following ways –

  1. It is still accessible and user-friendly for any researcher, irrespective of their bioinformatics skills, or their knowledge of computer programming language.

  2. They support a wide range of functions and applications including whole genome sequencing, whole exome sequencing, targeted gene sequencing, epigenetic studies, metagenomic studies, and de novo sequencing.  

  3. They are capable of integrating with multiple standardized NGS sequencing platforms used by leading research labs.

  4. Their reporting system includes easy-to-interpret data formats that can be shared quickly and easily across various platforms. 

While choosing a platform for your NGS data analysis, always check their testimonials and reviews. It is better to work on a platform that has worked with multiple peer-reviewed journals in the past. Working with such a platform ensures that you will always receive the analytics reports on or before time, complete with a publication-ready format.

How is the advent of automated NGS data analysis pipelines helping researchers?

The ideal NGS data analysis software is always scalable. It should be able to provide sequence analysis service to multiple fields, including pharma research, clinical studies, and genomics research with minimum bias. Most importantly, the commercial yet professional software platforms offer extensive support for the scientist community by the scientist community. In case, the user has queries or doubts regarding any step in the analysis process, a community of dedicated scientists is ready to answer their technical questions.  

The modern NGS data analysis software interfaces now available online are bridging the gap between the service and the user. The advanced communication and troubleshooting options are making the workflow much smoother for researchers than they were even a decade ago. Today, sequencing the entire human genome can take only one or two days and less than $1500 depending on the sequencing technique used thanks to the advanced NGS analysis software APIs available. Additionally, they promise better quality control and they offer reproducible data ready for all future audits. 

 

Published by Matthew Piggot