As part of our commitment to making genome sequencing more accessible we’re announcing support for CRAM files, in addition to FASTQs, as input to our analysis pipeline.

Now CRAM files straight out of Ultima machines, or any other source, can be used to save on storage and run analysis more efficiently.

This new feature can be used via S3 import.

Ultima integration

To make it easier to get insights from your data we’re partnering with Ultima to offer seamless integration.

The workflow is simple:

1. Configure your Ultima machine to write outputs to S3.
2. When sequencing finishes your CRAMs are uploaded to S3.
3. Import your files to Gencove.

Gencove will make sure the Reference Genome matches the one used for generating the CRAMs and proceed with analysis.

Ingesting CRAMs

Gencove offers support to ingesting CRAMs using the Web Dashboard or the Gencove CLI.

To import via the Web dashboard follow the tutorial in our docs to setup S3 integration and when starting analysis remember to set the input format as “CRAM”.

Alternatively, after you’ve completed the S3 integration setup, our CLI also offers an option to import CRAM samples.

In any of the cases, if input format is omitted Gencove will autodetect whether the samples are CRAMs or FASTQs and proceed accordingly.

Reach out to learn more about how you can use CRAMs to streamline your genomic analysis.