Navigation Links
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, and integrate more cleanly with other tools.

"Samtools 1.0 embeds CRAM into genomic data analysis pipelines and removes the need for additional processing," says Dr John Marshall, from the Sanger Institute. "This development paves the way for widespread uptake of this highly efficient file format in genomic research and will lead to lower storage costs."

The significant savings in storage that can be achieved are due to incorporating data compression techniques developed jointly by the Sanger Institute and the EMBL-European Bioinformatics Institute.

"It has been exciting to work on implementing CRAM into Samtools," says James Bonfield, at the Sanger Institute. "The great flexibility of CRAM has allowed a number of new compression techniques to be incorporated, which when combined with Samtools 1.0 will help to future-proof genomic data storage and analysis."


'/>"/>

Contact: Mark Thomson
mt9@sanger.ac.uk
44-122-371-0865
Wellcome Trust Sanger Institute
Source:Eurekalert

Related biology news :

1. New funding supports search for solutions to white-nose syndrome
2. NOAA, EPA-supported scientists find average but large Gulf dead zone
3. Supportive moms and sisters boost female baboons rank
4. NSF grant to Wayne State supports new concept for manufacturing nanoscale devices
5. Widespread support for rapid HIV testing in dental surgeries -- new study
6. Virus infection supports organ acceptance
7. Pew grants 22 young scientists support for biomedical research
8. Report supports shutdown of all high seas fisheries
9. Phase 3 study strengthens support of ibrutinib as second-line therapy for CLL
10. Information technology can simplify weight-loss efforts; social support still important for success
11. Surveys find that despite economic challenges Malagasy fishers support fishing regulations
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:2/11/2016)... Feb. 11, 2016  Vigilant Solutions announces today that its ... being used by Lee,s Summit Police ... location and arrest of a homicide suspect. ... covers around 65 square miles and is home to roughly ... has a single mobile license plate reader system and also ...
(Date:2/10/2016)... February 10, 2016 ... to 2016 iris recognition market report, combined ... is more widely accepted for border control. ... fingerprint and iris recognition technology in a ... avoid purchasing two individual biometrics devices. ...
(Date:2/9/2016)... AWRE ), a leading supplier of biometrics software and services, ... December 31, 2015.  --> --> ... an increase of 61% compared to $4.3 million in the same ... was $2.6 million compared to $0.2 million in the fourth quarter ... Higher revenue and operating income in the fourth quarter of this ...
Breaking Biology News(10 mins):
(Date:2/11/2016)... Feb. 11, 2016  Vermillion, Inc. (NASDAQ: VRML ... today announced the formation of the Steering Committee for ... --> Pelvic masses can present physicians ... management. Once pregnancy is ruled out, pelvic masses may ... advanced endometriosis, benign ovarian tumors and gastrointestinal and urinary ...
(Date:2/11/2016)... Germany and GERMANTOWN, Maryland ... ; Frankfurt Prime Standard: QIA) today announced the introduction ... for gene expression profiling, expanding QIAGEN,s portfolio of Sample ... enable researchers to select from over 20,000 human genes ... interactions between genes, cellular phenotypes and disease processes. ...
(Date:2/11/2016)...  Bioethics International, a not-for-profit organization focused on the ethics ... made accessible to patients around the world, today announced that ... publication of the Good Pharma Scorecard an ... as one of BMJ Open ,s ,Most Popular Articles, ... most frequently read. Ed Sucksmith , assistant editor ...
(Date:2/11/2016)... , Feb. 11, 2016  Spectra BioPharma Selling Solutions ... that provides biopharma companies the experience, expertise, operational ... deploy outsourced sales teams. Created in concert with ... both the strategic and tactical needs of its ... solutions through both personal and non-personal promotion. ...
Breaking Biology Technology: