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, effcient 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.
Highlights
Reference-free single nucleotide polymorphisms (SNPs) 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
SNP calling pipelines rely on a reference genome It is no overstatement to say that the recent technological advances that have made it possible to sample whole genomes many times over has changed forever the way that geneticists and genomicists design and carry out their experiments. Many of these experiments require the detection of genetic variants as a preliminary, most often single nucleotide polymorphisms (SNPs)
The predominant model for this is to have a single genome assembly chosen as the baseline against which all others will be compared. Often this reference genome will have been produced in a large-scale ‘big-biology’ project by a large consortium using long read Sanger-style sequencing or a hybrid approach that mixes long and short reads, but the defining characteristic will be that a great deal of time and expense has gone into preparing the reference
Summary
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.
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