#CRAM4GH Twitter chat: recap

9 Apr 2019

On Friday April 5, GA4GH held the #CRAM4GH Twitter chat. Guest “panelists” and experts James Bonfield, Thomas Keane, and Ewan Birney helped answer questions on the CRAM file format for genomic data compression.

#CRAM4GH Twitter Chat

On Friday April 5th, GA4GH held a live Twitter chat on the CRAM file format for genomic data compression. Leveraging the #CRAM4GH hashtag, the discussion featured guest experts James Bonfield, Principal Software Developer at the Wellcome Sanger Institute and lead CRAM maintainer, Thomas Keane, Team Leader at EMBL-EBI and co-lead of the GA4GH Large Scale Genomics Work Stream, and Ewan Birney, Director of EMBL-EBI and GA4GH chair, who answered questions from the community about the file format.

Visit the #CRAM4GH conversation reel to explore the full Twitter Chat, or view the highlights below.

CRAM is…

A file format that uses various algorithms to compress genomic data. By storing parts of a sequence that are different from a reference sequence, CRAM keeps files small and easily accessible.

 

CRAM’s impact extends beyond the genomics research community.

As genome sequencing becomes more routine, storing data efficiently and sustainably is essential. CRAM has immediate savings opportunities for the wider community:

While requiring careful attention to data access controls and permissions,  clinical genomics collaborators also stand to benefit by converting to CRAM. In response to question from @GeneFiddler, (Hywel Williams of Cardiff University) on the feasibility of adding CRAM support to clinical diagnostic pipelines, all three panelists emphasized interoperability already present in the system:

 

Open standards ensure the ongoing integrity and quality of scientific data.

Like all GA4GH standards, CRAM is developed and maintained within an open forum, enabling greater collaboration and evolution of data analysis. Our panelists shared their reasons for supporting open standards and open software:

 

In the future, CRAM will be smaller and faster.

The current version of CRAM (V3.0) reduces disk space by 30-50% compared to BAM. Bonfield envisions even greater storage savings with future versions, as well as support for additional data types:

Community members are invited to share ideas for CRAM V4 here:

Learn more about CRAM at ga4gh.org/cram/.

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