The Scramble conversion tool

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%. Av...

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Detalles Bibliográficos
Autor principal: Bonfield, James K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173023/
https://www.ncbi.nlm.nih.gov/pubmed/24930138
http://dx.doi.org/10.1093/bioinformatics/btu390
Descripción
Sumario: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. Contact: jkb@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

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