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The Scramble conversion tool.

James K Bonfield1

  • 1DNA Pipelines, Wellcome Trust Sanger Institute, Cambridgeshire, CB10 1SA, UK.

Bioinformatics (Oxford, England)
|June 16, 2014
PubMed
Summary
This summary is machine-generated.

Scramble, a new C implementation for SAM, BAM, and CRAM file I/O, offers significant file size savings (34-55%). This bioinformatics tool provides faster encoding than Java but slower decoding compared to BAM.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The standard reference implementation for the CRAM file format is Java-based.
  • Existing implementations may present performance or efficiency challenges in genomic data processing.

Purpose of the Study:

  • Introduce 'Scramble', a novel C implementation for Sequence Alignment Map (SAM), Binary Alignment Map (BAM), and Compressed Reference-Aligned Observation (CRAM) file input/output (I/O).
  • Evaluate the performance and efficiency of the C implementation against existing methods.

Main Methods:

  • Developed 'Scramble' as a C-language implementation for SAM, BAM, and CRAM file I/O operations.
  • Benchmarked the performance of 'Scramble' for encoding and decoding CRAM files.

Main Results:

  • The C implementation demonstrates file size reductions ranging from 34% to 55% compared to BAM.
  • Encoding CRAM files with 'Scramble' is 1.8–2.6× faster than BAM.
  • Decoding CRAM files is 1.5–1.7× slower than BAM.

Conclusions:

  • 'Scramble' offers substantial file size compression for genomic data.
  • The C implementation provides a performance trade-off, excelling in encoding speed while being slower in decoding compared to BAM.