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. 2014 Oct;30(19):2818-9.
doi: 10.1093/bioinformatics/btu390. Epub 2014 Jun 14.

The Scramble conversion tool

James K Bonfield  1
Affiliations

The Scramble conversion tool

James K Bonfield. Bioinformatics. 2014 Oct.

Abstract

Motivation: The reference CRAM file format implementation is in Java. We present 'Scramble': a new C implementation of SAM, BAM and CRAM file I/O.

Results: The C implementation of for CRAM is 1.5-1.7× slower than BAM at decoding but 1.8-2.6× faster at encoding. We see file size savings of 34-55%.

Availability and implementation: Source code is available at http://sourceforge.net/projects/staden/files/io_lib/ under the BSD software licence.

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Figures

Fig. 1.
Fig. 1.
Real time taken to convert from 230 Gb BAM to BAM (Scramble, Samtools) and BAM to CRAM (Scramble) formats. The system was a 16 core 2.2 GHz Intel Xeon E5-2660 with a local RAID XFS file system. Tests on slower disks and with smaller locally cached data files are in the Supplementary Material, including benchmarks of Sambamba (https://github.com/lomereiter/sambamba) and Biobambam (Tischler and Leonard, 2013)
See this image and copyright information in PMC

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