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FIGG: Simulating populations of whole genome sequences for heterogeneous data analyses

Sarah Killcoyne and Antonio del Sol*

Author Affiliations

Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 7, avenue des Hauts fourneaux, Esch/Alzette L-4362, Luxembourg

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BMC Bioinformatics 2014, 15:149  doi:10.1186/1471-2105-15-149

Published: 19 May 2014

Abstract

Background

High-throughput sequencing has become one of the primary tools for investigation of the molecular basis of disease. The increasing use of sequencing in investigations that aim to understand both individuals and populations is challenging our ability to develop analysis tools that scale with the data. This issue is of particular concern in studies that exhibit a wide degree of heterogeneity or deviation from the standard reference genome. The advent of population scale sequencing studies requires analysis tools that are developed and tested against matching quantities of heterogeneous data.

Results

We developed a large-scale whole genome simulation tool, FIGG, which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations. For normal variations we used publicly available data to determine the frequency of different mutation classes across the genome. FIGG then uses this information as a background to generate new sequences from a parent sequence with matching frequencies, but different actual mutations. The background can be normal variations, known disease variations, or a theoretical frequency distribution of variations.

Conclusion

In order to enable the creation of large numbers of genomes, FIGG generates simulated sequences from known genomic variation and iteratively mutates each genome separately. The result is multiple whole genome sequences with unique variations that can primarily be used to provide different reference genomes, model heterogeneous populations, and can offer a standard test environment for new analysis algorithms or bioinformatics tools.

Keywords:
Genome sequence; Simulation; Variation frequency; Population