MinION Mk1B IT requirements

MinION Mk1C IT requirements

GridION Mk1 IT requirements

PromethION 24/48 IT requirements

The EPI2ME platform (created by Metrichor Ltd., a subsidiary of Oxford Nanopore Technologies) offers a number of workflows for end-to-end analysis of nanopore data.

In a typical experiment, the user would prepare a DNA or RNA library for sequencing on a nanopore sequencing device. The sequencing experiment is started from the MinKNOW software, which controls the device and translates the electrical signals from each DNA/RNA read into basecalled sequences. The sequences for each read are saved in the .fast5 or FASTQ file format.

The basecalled FASTQ files can then be uploaded to the EPI2ME platform via a piece of software called the EPI2ME Agent. The user selects a workflow in the Agent such as 16S alignment, and the Agent transfers the read files one by one into the cloud for real-time analysis.

The analysis results are generated and updated in real-time in the form of a report in the EPI2ME platform.

Users can navigate to the EPI2ME portal from https://epi2me.nanoporetech.com to manage profile information, account details, and access their analysis reports and datasets.

Clicking on Open report displays the analysis report and information about the run:

The Quick view button shows the workflow version and some basic details.

Clicking Learn more ... opens up a detailed description of the workflow, with links to an example report, example datasets, citations and Nanopore Community release notes.

There are three types of datasets:

• Source: the raw data uploaded to EPI2ME. Every time you upload files to EPI2ME for analysis, a Source dataset will be created.
• Output: files/sequences/metadata produced during each discrete step of an analysis. For example, there will be a separate dataset created for the barcoding step, and another one for e.g. metagenomic classification.
• Reference: a special type of output produced by the FASTA Reference Upload workflow that can be used as reference sequence database for custom alignment analysis.

All datasets are temporarily available to view from the Analysis page while the analysis is running. After the analysis is complete, you have the option of saving the dataset to the EPI2ME cloud indefinitely. Only datasets that are stored in EPI2ME can be viewed in the Dataset dashboard. Storage of datasets in EPI2ME is optional and free, but may incur extra costs in future.

Datasets not stored in EPI2ME will be deleted from the platform (whichever is first):

• Within 24 hours of the analysis being stopped
• In line with our data retention policy for analyses that are left to run indefinitely (see https://metrichor.com/ig.html#dataretention)
  

Clicking Go to dataset opens a more detailed view and allows dataset management:

• Sharing the dataset with other EPI2ME users
• Storing the dataset in the cloud
• Reusing the dataset for a new analysis in EPI2ME
• Deleting the dataset

The Profile tab shows the user's details and the API keys.

Account details allows you to view the full list of people associated with an account, and to enable or disable sharing of analysis reports and datasets between participants.

Ask the Community takes you to the Nanopore Community, where you can ask questions and get support with your sequencing experiments.

Operating region allows you to switch between different operating regions.

The EPI2ME Agent communicates with the EPI2ME platform API over secure https both to execute analyses and to transfer data files in and out. The Agent is configured using a user's credentials for the platform to enforce security access controls. The Agent also has rudimentary capabilities for filtering returned files post-analysis.

The CLI Agent can be downloaded from https://epi2me.nanoporetech.com/software

When installing the EPI2ME Agent for the first time, a registration must be entered on the home page. The registration code is obtained from the EPI2ME website and is needed to validate the user.

Once the code has been entered successfully, the New analysis tab becomes clickable and an analysis can be started.

The Settings page shows the profile that is currently in use, and information about the data input/output folders, network, and the version of the Agent.

The appropriate analysis for the experiment can be chosen and run from the Analysis list.

In this section, the user can configure the analysis parameters.

Once the initialisation is complete, the Agent will begin securely uploading sequence data into the EPI2ME portal. The analysis begins as soon as the first batch of sequence data is successfully uploaded. A subset of the analysis report can be viewed either in the Agent itself, or the full report can be viewed by clicking the View report button (enabled only when reports are available), which directs the user to the EPI2ME portal.

If data is uploaded in batches, the report will be updated periodically to enable users to monitor the progress of the analysis in real-time.

The analysis can be stopped at any time with the Stop upload button to only stop file upload, or Stop analysis to stop both file upload and analysis.

The Upload/download progress section will display the amount of already-uploaded data and number of files and reads that have been uploaded.

Once a report becomes available, it is shown as a summary in the Agent. A more detailed report is available from the EPI2ME portal.

The report in the Agent also links to the Output directory, Analysis workflow documentation page, and the Input directory.

If there is any problem with the EPI2ME Agent or data analysis, you can click the bug icon (shown in the red box) on the interface to send a report.

Alternatively, navigate to Report a bug in the EPI2MEAgent application menu. You can also access the log files from here.

The Desktop Agent manages the data exchange of basecalled reads between the host computer and the EPI2ME analysis workflows. To download the Desktop Agent software, an EPI2ME account needs to be set up; this will include generating an alphanumeric registration code for a particular user. Opening the account involves logging into the EPI2ME website using the email address and password which are also used to access the Nanopore Community.

During runs both MinKNOW and the Desktop Agent require access to the AWS IP ranges currently listed here for the region eu-west-1, and also access to:

178.79.175.200

96.126.99.215

Windows/macOS

If logged in at the EPI2ME portal (http://epi2me.nanoporetech.com), updates can be found on the Software page.

If there is a critical update available, a pop-up message will appear when the EPI2ME Agent is launched. You will be required to download the new version to continue using the software.

For non-critical updates, a pop-up will appear recommending an update, but with the option to skip installing the new version of the Agent.

Linux

If you use Linux and have installed EPI2ME via the command line, follow the installation instructions described in Installing the Desktop Agent for Linux to perform any updates.

The EPI2ME Agent is an independent application that works from a folder of files. It can be run any time after a MinKNOW™ run has been started, including after the MinKNOW run has finished. There is also no requirement to have a MinION plugged in to run the Agent. Users must have an Oxford Nanopore Technologies account and log into the EPI2ME website at least once before being able to create a profile in Agent.

Multiple profiles can be associated with one account. You can switch to a different profile by clicking Use profile next to your profile of choice, or create a new one by clicking the Create profile button.

Clicking on a profile box presents the options to either use the profile for the next EPI2ME analysis, or to delete the profile.

Note: Exercise caution in deleting profiles, as this action cannot be undone.

If there is any problem with the EPI2ME Agent or data analysis, you can click the bug icon (shown in the red box) on the interface to send a report.

Alternatively, navigate to Report a bug in the EPI2MEAgent application menu. You can also access the log files from here.

You are able to store, manage, reanalyse and download data in the EPI2ME platform using the EPI2ME Data Manager. The EPI2ME Data Manager is a collection of web-based tools, services and interfaces that allow easy management of data associated with analyses uploaded to and run on the EPI2ME platform.

To create a new analysis, you need to provide Oxford Nanopore sequence files generated by the MinKNOW software as input and select an EPI2ME workflow. EPI2ME workflows are composed of several steps. Each step represents a logical unit of computation and/or analysis. Sequence data uploaded to the EPI2ME platform progress from one step to the next until all data have been processed (or you stop the analysis). The output of each step comprises one or more files that might include metadata, reference data, alignments (BAM), taxonomic classifications, basecalled sequences, etc. The files uploaded to EPI2ME and the collection of files output by each step of the workflow are each represented in EPI2ME as a reusable, sharable “Dataset”. Datasets are made available and managed in the EPI2ME Portal interface.

The EPI2ME platform is accredited to the ISO/IEC 27001 standard and your data will be encrypted in transit and at rest from the moment it is uploaded to the moment it is finally deleted. Datasets will not be stored in EPI2ME unless explicitly requested by the data owner. Datasets not explicitly stored are removed in accordance with our data retention policy. For full details about the security of your data in EPI2ME, please refer to our information governance document.

Datasets are accessed and managed from the data manager on the EPI2ME Portal website - a collection of tools and interfaces that allow you to store and manage files uploaded to EPI2ME or the collection of files that are output by each step of a workflow. You can view your own and shared datasets from the Datasets tab in the Portal:

All datasets are temporarily available to view from the Analysis page while the analysis is running. After the analysis is complete, you have the option of saving the dataset to the EPI2ME cloud indefinitely. Only datasets that are stored in EPI2ME can be viewed in the Dataset dashboard. Storage of datasets in EPI2ME is optional and free but may incur extra costs in future.

Datasets not stored in EPI2ME will be deleted from the platform (whichever is first):

• Within 24 hours of the analysis being stopped
• In line with our data retention policy for analyses that are left to run indefinitely (see https://metrichor.com/ig.html#dataretention )

Datasets can also be deleted at any time.

• Source: the raw data uploaded to EPI2ME. Every time you upload files to EPI2ME for analysis, a Source dataset will be created.
• Output: files/sequences/metadata produced during each discrete step of an analysis. For example, there will be a separate dataset created for the barcoding step, and another one for e.g. metagenomic classification.
• Reference: a special type of output produced by the FASTA Reference Upload workflow that can be used as reference sequence database for custom alignment analysis.

• Dataset type: Source, Output or Reference - described above
• Workflow name: the workflow run in EPI2ME which created the dataset
• Analysis: link to the analysis report
• Tags: these are entered during analysis set-up in the EPI2ME Agent, and can be edited in the Portal
• Created: the date on which the dataset was created
• Size: this changes dynamically as data is uploaded into EPI2ME or is analysed
• Stored in cloud or Expiring: if the dataset has not been permanently saved, it will be marked as "Expiring" until it is automatically deleted. Saved datasets are marked as "Stored in cloud"
• Owner: the person who ran the workflow that generated the dataset

There are several ways to manage a dataset:

• Share the dataset with all other EPI2ME users (including users outside of one's own account)
• Re-use the dataset for a new analysis in EPI2ME
• Store the dataset in the cloud
• Copy the dataset to another EPI2ME-enabled region
• Download the dataset contents
• Delete the dataset

Only datasets that are saved in EPI2ME can be reused to launch new analyses. Your data is uploaded to the EPI2ME platform once, then as new versions of software become available or new analysis workflows are released, you can re-analyse your data by running new workflows on your existing datasets. The choice of which analysis users are able to run is restricted to those analyses that are compatible with the dataset and its contents.

Setting up a new analysis from a dataset in the Portal mimics the analysis set-up in the EPI2ME Agent:

Please be aware that EPI2ME operates in multiple geographic regions, and analyses can only be run from datasets within the same EPI2ME-enabled operating region.

Important note: analyses can be stopped from within the Portal before completion, and users will be presented with an option to optionally store temporary datasets:

However, old versions of the EPI2ME Agent do not offer this functionality, and stopping an analysis in the Agent will automatically delete datasets in the EPI2ME portal. To mitigate this, you will need to indicate in the Portal which datasets are to be stored, before stopping the analysis either in Portal or in the Desktop Agent.

To switch to another EPI2ME-enabled region you can either change the preferred Operating region from the profile menu or you can change your preferred Operating region in your user profile by clicking the blue profile button > Profile option > Operating region option.

In order to copy an existing dataset to or from other regions, you will first have to ensure that:

1. You have the appropriate access to view and manage the selected dataset.
2. The analysis that generated the dataset has been stopped.
3. The dataset of interest has been stored in the EPI2ME platform.

The actions panel for a dataset will change depending on whether that dataset is stored in your current operating region. If the dataset is in your region then you will have access to a number of actions on that dataset including a new Copy dataset to button. However, if the operating region is different to that of the dataset you will be presented with the simpler actions panel and a Copy dataset here button. Below compare the two different routes whereby you will be able to copy datasets into other operating regions.

If the dataset is in the current operating region

Click Copy dataset to:

Dataset copy successfully finished:

If the dataset is outside the current operating region

Click Copy dataset here:

Dataset copy successfully finished:

If a dataset is available in the current operating region, the region label will be emphasised in bold.

Datasets can contain a very large number of files and the process of copying them into other regions will take time. You will be notified through the EPI2ME notification system when all files have been successfully copied after which the usual actions (Start analysis, download, share etc.) will become available.

If you have copied a dataset into other EPI2ME-enabled regions, you will be presented the option of which operating region you would like to delete datasets from. To begin deleting datasets, click on Delete dataset. You will then be presented with a panel with the various copies (replicas) listed. Datasets that are still in the process of being copied cannot be deleted and are distinguished by a Currently replicating label. As with the dataset details, the dataset that is in the current operating region is emphasised in bold. Select the dataset replicas you want to delete and click Delete replicas.

EPI2ME: A cloud-based bioinformatics and analytics platform developed by Metrichor Ltd. EPI2ME Portal: A web portal in which users can view and manage data held in EPI2ME. Data manager: The collection of tools services and interfaces for managing the output of EPI2ME workflows. Dataset: A collection of files and folders representing the analysis output of each discrete step in an EPI2ME workflow. Reference dataset: A dataset created by running the FASTA Reference Upload workflow that can be used in custom reference alignment workflows as the reference data.

The Command-line Agent allows the control of Nanopore analysis from the command line instead of a user interface. It contains the full functionality of the Desktop Agent, and is available for the Mac OS X, Linux and MS Windows operating systems. The Agent allows running several analyses simultaneously on one machine, operating from a server without a user interface, and automating analyses.

Commands are composed in the format <epi2me-binary-name> CATEGORY ACTION. For example (assuming the binary has been renamed to epi2me):

epi2me workflows list

will display a list of workflows, and

epi2me workflows run

will execute a specified workflow.

• accounts - View the accounts associated with the current user
• datasets - View and download datasets
• instances - Get the telemetry for a workflow instance
• products - View products, create new products and add workflows to products
• profiles - View, edit and create EPI2ME profiles
• settings - View and modify the configuration of the local application and your user account
• workflows - View workflows and start new instances

In addition, there are two utility categories relating to the application itself:

• version - Display the software version
• help - Display help

Help is available at every level of the application and is accessed by adding the keyword help at the end of any command. Help has the general form:

• <epi2me-binary-name> help
• <epi2me-binary-name> CATEGORY help
• <epi2me-binary-name> CATEGORY ACTION help

> ./epi2me-3.0.0-6800812 workflows detail help Get the details of a workflow

USAGE: epi2me workflows detail [options] [arg1]

EXAMPLES: epi2me workflows detail epi2me workflows detail $WORKFLOW_ID epi2me workflows detail $WORKFLOW_ID --docs

COMMANDS: help Display help version Display version

OPTIONS: --apikey An apikey to use for authentication instead of a profile. Must be used with a apisecret. --apisecret An apisecret to use for authentication instead of a profile. Must be used with a apikey. --docs Print the documentation for the workflow, if it exists. --h, --help Output usage information --product ID of the product to use. --profile The name of a local user profile to use for authentication. --proxy Address of a network proxy to use. --quiet Disable interactive prompts and omit supplementary output. --region The region to run the given command in. --v, --version Output the version number --workflow ID of the workflow to use.

> ./epi2me-3.0.0-6800812 workflows help View workflows and start new instances

USAGE: epi2me workflows [options] [command]

EXAMPLES: epi2me workflows epi2me workflows list epi2me workflows run $INPUT_1 $INPUT_2 ... $INPUT_N epi2me workflows detail epi2me workflows detail $WORKFLOW_ID epi2me workflows detail $WORKFLOW_ID --docs epi2me workflows favourite epi2me workflows favourite $WORKFLOW_ID epi2me workflows unfavourite epi2me workflows unfavourite $WORKFLOW_ID

COMMANDS: detail Get the details of a workflow favourite Favourite a workflow help Display help list List all the available workflows run Start a new analysis unfavourite Unfavourite a workflow version Display version

OPTIONS: -h, --help Output usage information -v, --version Output the version number

> ./epi2me-3.0.0-6800812 help USAGE: epi2me [options] [command]

EXAMPLES: epi2me accounts epi2me accounts list epi2me datasets epi2me datasets list epi2me datasets detail epi2me datasets detail $DATASET_ID epi2me datasets download epi2me datasets download $DATASET_ID epi2me datasets download $DATASET_ID $DESTINATION_FOLDER epi2me profiles epi2me profiles list epi2me profiles register epi2me profiles register $REGISTRATION_CODE epi2me profiles register $REGISTRATION_CODE --name $PROFILE_NAME epi2me profiles delete epi2me profiles delete $PROFILE_NAME epi2me profiles rename epi2me profiles rename $OLD_PROFILE_NAME epi2me profiles rename $OLD_PROFILE_NAME $NEW_PROFILE_NAME epi2me instances epi2me instances list epi2me instances detail epi2me instances detail $INSTANCE_ID epi2me products epi2me products list epi2me products workflows epi2me products workflows $PRODUCT_ID epi2me settings epi2me settings get region epi2me settings get disablePrompts epi2me settings get profile epi2me settings get admin epi2me settings get proxy epi2me settings get analytics epi2me settings change region epi2me settings change region $REGION_NAME epi2me settings change disablePrompts $DISABLE_PROMPTS epi2me settings change profile epi2me settings change profile $PROFILE_NAME epi2me settings change admin $IS_ADMIN epi2me settings change proxy $PROXY epi2me settings change analytics $ENABLE_ANALYTICS epi2me settings list epi2me workflows epi2me workflows list epi2me workflows run $INPUT_1 $INPUT_2 ... $INPUT_N epi2me workflows detail epi2me workflows detail $WORKFLOW_ID epi2me workflows detail $WORKFLOW_ID --docs epi2me workflows favourite epi2me workflows favourite $WORKFLOW_ID epi2me workflows unfavourite epi2me workflows unfavourite $WORKFLOW_ID

COMMANDS: accounts View the accounts associated with the current user datasets View and download datasets help Display help instances Get the telemetry for a workflow instance products View products, create new products and add workflows to products profiles View, edit and create epi2me profiles settings View and modify the configuration of the local application and your user account version Display version workflows View workflows and start new instances

OPTIONS: -h, --help Output usage information -v, --version Output the version number

epi2me accounts list

epi2me workflows detail $WORKFLOW_ID

This is analogous to starting a new analysis in EPI2ME where the user is interactively led through the process. The command to run in interactive mode takes the following form:

epi2me workflows run $INPUT_1 ... $INPUT_N

Here is a screenshot of a new analysis that was started interactively where the user is able to modify the settings at every step as they would in the Desktop Agent:

• Multiple data sources as input
• Data sources contain no human data

epi2me workflows run $INPUT_1 ... $INPUT_N --nothuman --workflow $WORKFLOW_ID --account $ACCOUNT_NUMBER

epi2me workflows run $INPUT_1 ... $INPUT_N --consentedHuman --workflow $WORKFLOW_ID --account $ACCOUNT_NUMBER --output $OUTPUT_LOCATION --store --quiet