CSAM: Compressed SAM format - LIRMM - Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier
Journal Articles Bioinformatics Year : 2016

CSAM: Compressed SAM format

Abstract

Motivation: Next generation sequencing machines produce vast amounts of genomic data. For the data to be useful, it is essential that it can be stored and manipulated efficiently. This work responds to the combined challenge of compressing genomic data, while providing fast access to regions of interest, without necessitating decompression of whole files. Results: We describe CSAM (Compressed SAM format), a compression approach offering lossless and lossy compression for SAM files. The structures and techniques proposed are suitable for representing SAM files, as well as supporting fast access to the compressed information. They generate more compact lossless representations than BAM, which is currently the preferred lossless compressed SAM-equivalent format; and are self-contained, that is, they do not depend on any external resources to compress or decompress SAM files. Availability and Implementation: An implementation is available at https://github.com/rcanovas/
Fichier principal
Vignette du fichier
Canovas-bioinformatics-2016-btw543.pdf (409.2 Ko) Télécharger le fichier
Origin Publisher files allowed on an open archive
Loading...

Dates and versions

lirmm-01951638 , version 1 (11-12-2018)

Identifiers

Cite

Rodrigo Cánovas, Alistair Moffat, Andrew Turpin. CSAM: Compressed SAM format. Bioinformatics, 2016, 32 (24), pp.3709-3716. ⟨10.1093/bioinformatics/btw543⟩. ⟨lirmm-01951638⟩
107 View
115 Download

Altmetric

Share

More