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Samtools CRAMS in support for improved compression formats
Date:8/15/2014

Computer scientists at the Wellcome Trust Sanger Institute have released a major upgrade of Samtools, one of the most popular next-generation sequence analysis tools. The revised Samtools 1.0 enables researchers to easily compress, share and analyse genomic sequence data, reducing costs and supporting genomics research around the world.

The Global Alliance for Genomics and Health, in which the Sanger Institute is a partner, has been set up to enable researchers and clinicians to work together using standardised and efficient DNA sequence data formats to find the genetic variants responsible for disease. Samtools 1.0 supports this initiative by enabling researchers to read and write data in the new CRAM format, which was recently adopted by the Global Alliance, in addition to the existing SAM and BAM file formats for genomic sequence information.

The benefits of using CRAM are immediate: it gives a size reduction of 10-30 per cent. In addition, in a similar fashion to the JPEG format for images, CRAM supports much greater compression up to a hundred fold in "lossy" mode which preserves almost all of the important information.

"This major rebuild of Samtools reflects our commitment to supporting the global use of sequencing data," says Dr Richard Durbin, Head of Computational Genomics at the Sanger Institute. "Genome science worldwide relies on fast and efficient data analysis and storage, and Samtools 1.0 fulfils this need by supporting new sequencing and analysis technologies."

Samtools software is embedded in many bioinformatics pipelines and is the foundation of many thousands of genomic research papers. Since its creation in 2009, the program has been downloaded more than 225,000 times. Samtools 1.0 is freely available at http://www.htslib.org/. This new version was substantially rewritten to support the highly efficient genomic data format CRAM, add new functionality,
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Contact: Mark Thomson
mt9@sanger.ac.uk
44-122-371-0865
Wellcome Trust Sanger Institute
Source:Eurekalert

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