Abstract rendering of noise - Public Domain image from https://www.publicdomainpictures.net/en/view-image.php?image=277335&picture=sound-noise POD5 Files

This ONT service enhancement is available for all customers using our Long Read and Hybrid sequencing services.

Abstract rendering of noise - Public Domain image from https://www.publicdomainpictures.net/en/view-image.php?image=277335&picture=sound-noise

POD5 files can be provided for an additional fee of £10 per sample (excluding VAT). These files are uploaded directly to your project portal at the same time as your sequencing data becomes available.

Please note that, unlike sequencing data — which is retained for 12 months — POD5 files are available for download for 28 days only. Due to the large storage requirements, POD5 files are permanently removed after this period and cannot be retrieved.

Target turn around times for delivery of POD5 files is aligned to the sequencing service option you have purchased. You can check the target turn around times.

Some Frequently Asked Questions

What is a POD5 file?

POD5 files (formerly known as FAST5 files) contain the raw signal data generated during sequencing, specifically the electrical current measurements recorded as nucleic acids pass through the nanopores. This raw signal forms the basis of all downstream analysis.

Read files (FASTQ) are produced from POD5 files through a process called basecalling. FASTQ files contain only the inferred nucleotide sequences and associated quality scores, not the underlying raw signal data.

There are multiple computational models available for basecalling, and these models are updated frequently as accuracy and performance improve.

What can POD5 files be used for?

Access to POD5 files allows you to re-run basecalling at any time, either with updated basecalling models released in the future or with specialised models designed to detect DNA methylation. POD5 files are required for all re-basecalling workflows, whether or not methylation analysis is included.

Methylation involves the addition of a methyl group to adenine (A) or cytosine (C) bases and plays an important role in regulating gene expression. These modifications can influence key biological processes such as pathogenicity, antibiotic resistance, DNA repair, cell replication, and host defence.

DNA methylation machinery has been lost in various, distinct, evolutionary lineages. If you do not anticipate the need to re-run basecalling or perform methylation analysis in the future, retaining POD5 files may provide limited additional value.

Which MicrobesNG services is this applicable to?

POD5 file delivery is offered as an optional add-on service for NEW Long Read and Hybrid sequencing service orders only.

POD5 file delivery is not available for:

  • customers who have already received their sequencing data, or
  • orders where the POD5 option was not purchased in advance.

If you would like to receive POD5 files and have not yet submitted your samples, there is still time to add this option. Please contact us for further information on how to purchase POD5 file delivery.

I already have long read data from MicrobesNG, can I get POD5 files for those now?

Unfortunately no. This service enhancement is only available for new sequencing projects that have not received data.

How can I order POD5 files and how much do they cost?

Simply tick the 'POD5' box when requesting a quote from us.

£10 (ex VAT) for POD5 files per sample will automatically be added as a new line on the quote that we send you.

Receiving and Accessing your POD5 Files

Size & format

POD5 files are large and require considerable storage space - it’s reasonable to expect about 10 GB of storage required per sample, but this will vary depending on genome size and the total yield, so we advise having excess storage space available.

Files are provided in POD5 format and uploaded directly onto your project portal.

There will be multiple POD5 files per sample.

Availability of POD files

Each file is stored on the project portal and available for download at any time within a 28 day period.

File download after this 28 day period is not possible and the file will be removed from the project portal automatically.

If your access has nearly expired and you think you need an extension, please contact us.

I want other service enhancements, can I ask for those?

Absolutely, always ask! We evolve our services based on our customer needs, so let us know what you are looking for and where possible we will provide solutions for you. Contact us and let us know what you need or how we can help.

I’m interested in methylation - is there any information on that?

Yes and this service enhancement is coming soon! If you would like to register interest and help inform service design please complete our quick survey.

What happens if I send the samples in batches?

POD5 files will be produced when we provide your sequencing data, so if you send us your samples in batches you can expect the POD5 files to be provided in the resulting batches.

The 28 day access window for files applies to each batch separately.