EPI2ME: bioinformatics made simple

Even the smallest of organisms have genomes that are millions of bases long. The genome of Escherichia coli, for example, is approximately 4.6 million bases long¹, far too large to interpret manually. You need the right tools to make sense of it, and this is where bioinformatics comes in — the use of computational tools that transform a sequence of nucleotide bases into meaningful biological insights. However, learning to code or navigate complex pipelines is not always feasible, especially when you are focused on generating data in the lab. That is where EPI2ME comes in: a solution that can make sense of your sequencing and support data analysis for all levels of expertise.

In this Nanopore Know-How blog we will introduce EPI2ME and show how anyone can use it to take the challenge out of bioinformatics, gain control of their data, and have full oversight of their workflow, from data generation through to data analysis.

What makes data analysis challenging?

Once sequencing is complete, researchers face the obstacle of turning DNA and RNA sequencing data into meaningful insights. A wide range of bioinformatic tools are there for the job, but most require the use of the command line: a computer interface where you type instructions rather than using a point-and-click interface. Whilst it provides flexibility, learning how to use it effectively can be a steep and time-consuming learning curve.

Even with command-line skills, finding the right tool for the job is not always straightforward. GitHub is one example of a hosting platform where data analysis tools can be downloaded, but some tools are more reliable than others and not all of them are optimised for Oxford Nanopore data. Further to this is the issue of maintenance. Not all code is consistently updated, increasing the risk of errors over time and no one to turn to for support.

Due to these challenges, researchers may feel the need to pass their data on to a bioinformatics team, giving up control of analysis and losing visibility of their full workflow. If the bioinformatics team supports multiple departments, this can become a bottleneck and delay time to results.

Data analysis is an essential step within a researcher’s workflow, so is there an alternative to wrestling with command-line tools or waiting on busy teams?

What is EPI2ME?

EPI2ME is a desktop app that puts best-practice bioinformatic workflows at your fingertips. Just point and click to install and run workflows, either locally or in the cloud depending on what suits your setup. You can run these tools with confidence knowing they are fully supported by the Oxford Nanopore team. Some workflows can even be run in real time, during your sequencing run.

Each EPI2ME workflow will produce standard output files and interactive reports, so you can quickly check your data quality and analytical results and move toward answers faster. We will take a closer look at output files in a future Nanopore Know-How blog.

Have a bioinformatics background? EPI2ME still has you covered. The same workflows available via the EPI2ME app can be downloaded from GitHub to run as command-line tools. These EPI2ME workflows are developed using the Nextflow software, and the Oxford Nanopore team ensures that the pipelines are standardised.

For pipeline developers, custom Nextflow workflows hosted in GitHub can be easily imported in the EPI2ME app by simply providing the link to the repository. They can then be run using the point-and-click interface. This way, you can make your pipelines accessible to your colleagues who may not have bioinformatics experience, and to the whole Nanopore Community.

However you use EPI2ME, it provides comprehensive analysis in one platform. So, what research questions can it help you answer?

What can EPI2ME do?

Whether you are studying cancer, microbes, or transcriptomes, EPI2ME gives you ready-to-run workflows designed to deliver high-quality results. Currently, we have over 15 workflows tailored to common research applications, including:

• Basic tasks such as basecalling and alignment

• Genome assembly

• Human genomics

• Cancer genomics

• Microbiology and infectious diseases

• Targeted sequencing

• Single-cell and bulk transcriptomics

These workflows include tools for aligning reads, assembling genomes, calling variants, annotating genes, classifying species, and more. Our team of bioinformatics experts select each tool to deliver the best results for analysing Oxford Nanopore sequencing data, integrating these tools into pipelines so that they run seamlessly.

To explore the full range of workflows and see example reports, head to the EPI2ME website. Or better yet, why not download the EPI2ME app for free today and start to explore?

How do I get started?

Getting started with EPI2ME is simple. Download and run the EPI2ME installer package to launch the app. You can then click on the ‘Launch’ tab and find the workflow best suited to your research needs. Click install, then the workflow will be downloaded and saved on your machine, ready to run.

For analysis to begin, you need a dataset. If you have basecalled your data using MinKNOW, the software that controls our sequencing devices, reads will be saved to a user-defined location. No data yet? Demo data for all the workflows can be accessed in the EPI2ME app; there are also Oxford Nanopore open data sets that are free for you to explore.

Once your workflow is installed, choose whether to run it locally or in the cloud, select your dataset or the demo data, tweak the parameters in the launch wizard, and hit start. After the run, you can view the full report within the platform and access output files for further processing if needed.

Your first analysis could be today. Watch our masterclass on how to analyse your Oxford Nanopore data and start exploring with confidence.

Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.