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CARGO: effective format-free compressed storage of genomic information

2016; Oxford University Press; Volume: 44; Issue: 12 Linguagem: Inglês

10.1093/nar/gkw318

1362-4962

Łukasz Roguski, Paolo Ribeca,

Gene expression and cancer classification

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.