Introduction

The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats, sometimes inheriting from them suboptimal design choices; this hinders flexible and effective data sharing. Here, we present CARGO (Compressed ARchiving for GenOmics), a high-level framework to automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of our approach to FASTQ and SAM archives require a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors and scale well to multi-TB datasets. All CARGO software components can be freely downloaded for academic and non-commercial use from http://bio-cargo.sourceforge.net.

Publications

  1. CARGO: effective format-free compressed storage of genomic information.
    Cite this
    Roguski Ł, Ribeca P, 2016-07-01 - Nucleic acids research

Credits

  1. Łukasz Roguski
    Developer

    Algorithm Development, Centro Nacional de Análisis Genómico, Spain

  2. Paolo Ribeca
    Investigator

    Algorithm Development, Centro Nacional de Análisis Genómico, Spain

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Summary
AccessionBT000937
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionSpain
Submitted ByPaolo Ribeca