Transitioning From DNAnexus Classic

General FAQ

When will I no longer be able to upload new data to DNAnexus classic?

New uploads to DNAnexus Classic will not be allowed after December 31st, 2014.

When will DNAnexus Classic be completely retired?

March 31, 2015

Why is DNAnexus Classic being shut down?

The new DNAnexus platform has superseded DNAnexus Classic in technology and user base. We are now focused on accelerating platform development.

What Classic data can I move to the platform?

You can move the raw data over (the reads in FASTQ format). For more instructions on how to do this, please see our Answers forum here.

What are the main differences between DNAnexus Classic and the new DNAnexus platform?

DNAnexus Classic was built as a turnkey solution for biologists to run standard pipelines on DNA sequence data. In Classic, scientists upload their sequence data, select a pre-built pipeline from a list and click run.

The new DNAnexus platform provides users the ability to upload or build custom analysis pipelines by accessing the platform’s open API and SDK, working in either the command line or web environments. In addition, platform users can share data and tools, and collaborate on projects with other research labs around the world.

How can I migrate my reads into the platform?

You can move your raw data (the reads in FASTQ format) over to DNAnexus platform. To transfer your reads to the platform via the command line interface please review the following documentation.

If you prefer to work on a web interface, you can follow these steps to copy your files from Classic to the new DNAnexus platform.

Can I map my transferred data with a DNAnexus Classic mapper on the new platform?

Unfortunately, no. The new platform does not have direct one-to-one migration pipelines. However, the new platform provides a wide variety of different mappers in the App Page. Many users prefer the BWA-mem as it is one of the more modern mappers.

Can I run my Classic analyses on the new platform?

Unfortunately, the new platform does not have the exact same analysis functionalities as DNAnexus Classic. Once you move your raw data over you will be able to build your own pipeline from which you may select from a variety of apps listed in our Apps Library.

Moving forward you can run similar analyses on DNAnexus platform. We’ve built a simple exome workflow, which you can access here, explore your results with Dalliance, an interactive genome browser.

The screencast below explains how to use this workflow.

I have a project that is in a critical phase where switching to DNAnexus platform or to another system would be very difficult. Is there anyway to extend my DNAnexus Classic account?

A one month extension for uploading samples will be considered upon request. Please contact us directly at

I have credits on my Classic account. How will I be reimbursed?

If you paid for a sample to be stored beyond March 31, 2015, a refund check will be issued for the prorated balance based on the expiration date for each sample. Our finance department will be contacting you to confirm your refund payment information. If you have any questions regarding the refund process, please contact accounts receivable at

How much does the new DNAnexus platform cost?

The new platform follows a flexible pricing model, where you pay for the resources you use (i.e. any data transferred or stored, and any computation performed). All new platform users are provided with $125 of free credit, which should be sufficient to get you started.

Distributors FAQ

Can we keep the samples archived on Classic until the expiration date?

After March 31, 2015 we can move the data to the new platform for archival purposes only. Your customers will be able to access their data, however, they will not be able to run further analyses or modify the data on DNAnexus Classic.

Last edited by Thanh-Ha Nguyen (tnguyen), 2014-12-11 19:30:36