Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data

Table 1 Performance of the SpeedGene algorithm on the simulated datasets

SNPs	Size	PLINK	Gzip	SpeedGene	DNAzip (Extrapolated)	Avg MAF
1 million	3.731 GB	238 MB	22 MB	18 MB	16 MB + ∼ 4.2 GB reference	0.004944
30 million	112 GB	6.985 GB	592 MB	534 MB	310 MB + ∼ 4.2 GB reference	0.004228

Compressed file sizes of the simulated datasets using PLINK, Gzip, SpeedGene and DNAzip. Each dataset contains 1000 subjects.

ISSN: 1471-2105