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How can NGS software help cut down the time required for analysis of DNA sequencing data?

Posted August 17, 2019

When the rest of the world was busy decoding genomic sequences one nucleotide at a time, the Human Genome Project and the X-PRIZE competition inspired the development of a shotgun-based DNA sequencing technique in 2005. Known as the Next-generation sequencing or NGS technique, this method is capable of running massively parallel sequence analyses at a reduced cost.

Free image via Pixabay

Ever since the advent of NGS in 2005, genomics studies have gained a new impetus. Over the next decade and a half, several new NGS techniques have evolved. These include the Roche 454 system, SOLiD, and the Illumina GA/HiSeqy System. The Roche system has the highest read length, while the SOLiD has the best accuracy, and the Illumina system offers the biggest output of sequencing at the lowest cost of reagents.

How does NGS pose a new challenge for researchers?

The presence of commercially available software for the alignment and analysis of NGS data made the second generation sequencing techniques instantly famous in basic research. It has not only revolutionized genomics, but it now allows the researchers to conduct experiments previously deemed impossible or unaffordable.

Just like many other advanced technologies, NGS has its fair share of challenges. Even a medium-sized lab, with 10 to 15 researchers can generate more than one terabyte of NGS data per year from 500 NGS samples. Despite its significant contributions to the fields of genomics, transcriptomics, protein-DNA interactions, and epigenomics, NGS poses a substantial problem with the bulk of data it generates per round of sequencing.

Respite for research teams comes in the form of cloud computing. In the 21st century, when almost all leading corporations are moving their company’s critical data to the cloud, there is no reason for genomics to fall behind. Second-generation sequencing techniques coupled with cloud computing and web-based services, provide the research teams with high accuracy, secure data storage, rapid analysis, and safe import of analysis reports.

What should the best web-based NGS software services provide?

Cloud computing refers to an entire system of cloud infrastructure that people can access on-demand. It can provide IT resources and applications with easy application program interface (API). Several NGS software programs are now available on cloud computing based on pay-as-you-go pricing. These products and services often refer to networks, storage, servers, applications, and services that one can access without investing in any additional hardware. NGS alignment and analysis via the cloud are ideal for small to medium-sized labs that lack the funds to set up dedicated NGS data analysis systems.

The best NGS analysis via the web should have the following features –

1. On-demand services

You should not have to seek help from bioinformatics engineers or service providers every time you need analysis services.

2. Pay-as-you-go

You need to pay only when you use their services.

3. Customization powers

When you need to alter parameters or include additional information, you should be able to do so at the API level.

4. Economical

A commercial, NGS cloud platform should be affordable. The classical NGS techniques that are depending on hardware show little adaptability towards scale-up or scale-down of NGS data.

5. Rapid turnaround

It makes little sense to export bulk data to another platform unless it can promise quick analysis and delivery of reports. The state-of-the-art NGS analysis cloud platform delivers results in a matter of hours.

Why should you try the new cloud-based NGS software and storage services?

In the case of the new-age NGS software-as-a-service (SaaS), the users have complete control over the OS and the APIs. The ability of these cloud-based services to extend to desktops and even mobile OSx makes them instantly accessible for teams across the globe. The ready availability of multiple services on one pay-as-you-use platform expedites the entire NGS data analysis and report generation process.

1. Standardized analytics pipelines

The commercial NGS software services provide all users with standardizes pipelines necessary for NGS data analysis. These come with flexible parameters, easy customization via API settings, and time-tested troubleshooting methods. That means no longer scouring manuals and going through each step of the set-up to find the snag in the analysis. The standardized pathways in the commercial NGS data analysis cloud services ensure that every user has access to the highest quality of alignment and analysis.

2. Add-on features and functions

The standard NGS software platform provides services like sequencing data storage, metagenomics analysis, mapping, de novo assembling, and library quality control. NGS analysis Software offers additional access to the genome browser, variant browser, and the variant summary for every DNA sequencing cycle. Variant calling is incredibly time-consuming and challenging due to the high diversity of the components. The easy-to-use and customize API makes variant calling a rather rapid and easy task.

3. Rapid analysis irrespective of data bulk

Additionally, it gives you the opportunity to check out the coverage plot for your whole genome or whole exome data. The complete analysis of a NGS data does not take more than a couple of hours with the latest techniques. Even with the highly affordable pay-as-you-go services, you can receive the complete report of an NGS data analysis experiment within an hour or two at the most. The ideal web-based NGS software for DNA sequence analysis should deliver the reports in a ready-to-print or publish format.

4. Wide range of compatibility

The biggest challenge that researchers face right now is the lack of harmony between the cloud-based analysis platforms and the bioinformatics tools. However, there are quite a few cloud-based bioinformatics platforms that provide NGS data analytics compatible with the standard FASTQ, FASTQ-SFF, and SAM/BAM formats. Most importantly, your unique and precious NGS data is entirely safe in the cloud storage environment. You can access your data, import it, or run analysis whenever you want in the future.

NGS software reduces the latent time between sequencing and alignment steps. It also catalyzes the analysis of NGS data by passing it through ready-to-use analysis pipelines. With high accuracy and low cost, NGS software platforms are here to write a new future for all branches of genomics.

Article source: Basepair


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