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Research & Development Request

Eurostars: SME to integrate efficient genome sequencing data compression and transport in genome analysis applications sought.

Country of Origin: Switzerland
Reference Number: RDCH20180716001
Publication Date: 16 July 2018

Summary

A Swiss bioinformatics SME developing encoders/decoders of genome sequencing data compliant with an ISO Standard for Genomic Data Representation and Transport (MPEG-G) seeks SME or industry partners for a Eurostars research cooperation. MPEG-G is a new ISO standard for the compression/transport of genome sequencing data. It aims at providing better performance than existing formats. The goal is to integrate the SME’s codecs in existing genome sequencing data analysis software applications.

Description

Genome sequencing volumes are expected to grow substantially, driven by falling sequencing costs and by the increasingly compelling clinical value of genomic information. Genome sequencing can be performed for research, diagnostics, individualized treatment and preventive health care.

 

The genome analysis pipeline, from sequencing to the interpretation of results, is evolving rapidly, with significant innovation along all stages, but it is still affected by inefficiencies and bottlenecks. While sequencing cost had been the main obstacle to large scale analyses in the past, today’s difficulties are more concentrated downstream and are related to the cost and complexity of data management. The ever-growing data volumes (with growth rates largely exceeding even Moore’s law), the size of individual genomic files, the diversity of the data formats at the different stages of the pipeline, the inefficiency of compression/decompression algorithms and the cost of storing and sharing data in a highly regulated environment (enforcing specific data protection policies) generate enormous challenges for research labs. While interpreting DNA information remains a highly complex task, many of the difficulties listed above are not intrinsic to the problem, but originated with the use of the inappropriate technologies in common practice.

  

The Swiss bioinformatics SME's enabling technology is specifically conceived to address these issues. It has been designed to simplify and reduce analysis costs and complexity, by standardizing and optimizing the native compressed format with which genomic data are represented for storage and sharing. In particular the start-up company is leading the development of a new Standard for Genomic Data Representation and Transport, called MPEG-G, currently in its final approval stage within the International Organisation for Standardisation (ISO). 



The SME is looking for companies currently developing applications which handle genome sequencing data. Such applications are those typically handling files in the FASTQ/BAM/CRAM formats. The company offers to integrate MPEG-G as an additional format to be supported as input/output format. Applications using proprietary formats are acceptable candidates as well if there is a clear business case.



These can include genome analysis service providers, genomic data repositories, clinical facilities providing genomic medicine services and any type of business utilizing data produced by genome sequencing machines.



The Swiss SME is providing the expertise in the development of the ISO standard and the implementation of compliant software and would like to partner with organisations wishing to integrate the new ISO standard in their existing applications.



They aim at responding to the Eurostar call with deadline on 13th September 2018. 

The deadline for expression of interests is 15th August 2018.

The consortium should be composed of a minimum of 2 SMEs from 2 different countries. A research cooperation is envisaged. 

The duration of the project should be between 24 and 30 months.

Requested partner

The specific area of activity of the partner: 

Company handling large amounts of genome sequencing data for 

- genomic analysis services

- genomic data storage

- genomic medicine



The tasks to be performed by the partner sought: 

Support for integration of the bioinformatics company’s software into the existing applications or workflows.