title: Reference-free SNP detection: dealing with the data deluge.
abstract: Reference-free SNP detection, that is identifying SNPs between samples directly from comparison of primary sequencing data with other primary sequencing data and not to a pre-assembled reference genome is an emergent and potentially disruptive technology that is beginning to open up new vistas in variant identification that reveals new applications in non-model organisms and metagenomics. The modern, efficient data structures these tools use enables researchers with a reference sequence to sample many more individuals with lower computing storage and processing overhead. In this article we will discuss the technologies and tools implementing reference-free SNP detection and the potential impact on studies of genetic variation in model and non-model organisms, metagenomics and personal genomics and medicine.
authors: Richard M
authors: RM
authors: Leggett
authors: Dan
authors: D
authors: MacLean
mesh_terms: D000818:Animals; D020451:Contig Mapping; D014644:Genetic Variation; D006801:Humans; D056186:Metagenomics; D008962:Models, Theoretical; D020641:Polymorphism, Single Nucleotide