journal cover

The Scramble conversion tool

Bioinformatics

Jun 16, 2014

James K Bonfield

Abstract

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

Mentioned in this Paper

Alkalescens-Dispar Group
CCRL2 gene
Computer Programs and Programming
DPYSL5 gene
Programming Languages
c new
Information Extraction
Genome, Bacterial
Genome, Human
Computers, Digital
14
1
39
Paper Details
References
  • References4
  • Citations14
1
  • References4
  • Citations14
12

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The Scramble conversion tool

Bioinformatics

Jun 16, 2014

James K Bonfield

PMID: 24930138

DOI: 10.1093/bioinformatics/btu390

Abstract

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

Mentioned in this Paper

Alkalescens-Dispar Group
CCRL2 gene
Computer Programs and Programming
DPYSL5 gene
Programming Languages
c new
Information Extraction
Genome, Bacterial
Genome, Human
Computers, Digital
14
1
39

Similar Papers Found In These Feeds

Structural Biology: Biophysics

Structural Biology: Biophysics describes the study of structural biology using various biophysical techiniques such as imaging, computational modeling, etc. Discover the latest research on structrual biology here.

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Nucleic Acids Research

Facing growth in the European Nucleotide Archive

Nucleic Acids ResearchDecember 4, 2012
Guy CochraneVadim Zalunin
Nucleic Acids Research

The Sequence Read Archive: explosive growth of sequencing data

Nucleic Acids ResearchOctober 20, 2011
Yuichi KodamaInternational Nucleotide Sequence Database Collaboration
Paper Details
References
  • References4
  • Citations14
1
  • References4
  • Citations14
12
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