title: CARGO: effective format-free compressed storage of genomic information.
abstract: 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.
authors.affiliation: Algorithm Development, Centro Nacional de Análisis Genómico, Carrer Baldiri i Reixac 4, Barcelona 08028, Spain Experimental and Health Sciences, Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, Barcelona 08003, Spain.
authors.forename: Łukasz
authors.identifier: 0000-0003-2764-962X
authors.initials: Ł
authors.lastname: Roguski
authors.affiliation: Algorithm Development, Centro Nacional de Análisis Genómico, Carrer Baldiri i Reixac 4, Barcelona 08028, Spain Integrative Biology, The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, United Kingdom paolo.ribeca@gmail.com.
authors.forename: Paolo
authors.identifier: 0000-0001-5599-3933
authors.initials: P
authors.lastname: Ribeca
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D044962:Data Compression / Q000379:methods; D016678:Genome; D023281:Genomics; D016247:Information Storage and Retrieval / Q000379:methods*; D012984:Software