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Identifying SNPs without a Reference Genome by Comparing Raw Reads

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String Processing and Information Retrieval (SPIRE 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6393))

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Abstract

Next generation sequencing (NGS) technologies are being applied to many fields of biology, notably to survey the polymorphism across individuals of a species. However, while single nucleotide polymorphisms (SNPs) are almost routinely identified in model organisms, the detection of SNPs in non model species remains very challenging due to the fact that almost all methods rely on the use of a reference genome. We address here the problem of identifying SNPs without a reference genome. For this, we propose an approach which compares two sets of raw reads. We show that a SNP corresponds to a recognisable pattern in the de Bruijn graph built from the reads, and we propose algorithms to identify these patterns, that we call mouths. We outline the potential of our method on real data. The method is tailored to short reads (typically Illumina), and works well even when the coverage is low where it reports few but highly confident SNPs. Our program, called KisSnp, can be downloaded here: http://alcovna.genouest.org/kissnp/ .

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Peterlongo, P., Schnel, N., Pisanti, N., Sagot, MF., Lacroix, V. (2010). Identifying SNPs without a Reference Genome by Comparing Raw Reads. In: Chavez, E., Lonardi, S. (eds) String Processing and Information Retrieval. SPIRE 2010. Lecture Notes in Computer Science, vol 6393. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16321-0_14

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  • DOI: https://doi.org/10.1007/978-3-642-16321-0_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16320-3

  • Online ISBN: 978-3-642-16321-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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