Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome

Abstract : Background / Purpose:Detecting Single Nucleotide Polymorphisms (SNPs) between genomes is a routine task with Next Generation Sequencers (NGS) data. SNP detection methods generally need a reference genome. As non-model organisms are increasingly investigated, reference-free methods are needed. The discoSnp method detects SNPs directly from raw NGS data set(s) without using any third-party information. The pea non-model organism has a 4.5 GB complex genome without reference. We compared, on the same set of low depth pea sequences, the SNPs generated by discoSnp with those published with a previous SNP discovery pipeline, and those generated using classical mapping approach with the association of Bowtie2 and GATK tools.Main conclusion:The quality of discoSnp results in association with its very low memory needs and low time footprints led us to choose this software for a SNP discovery and direct Genotypin. By Sequencing project on a set of 48 pea genomic DNA libraries from a recombinant inbred lines subpopulation sequenced with Illumina HiSeq2000 technology. The analysis enabled to identify 88,851 SNP polymorphs on this population, from which around 60k SNPs will be genetically mapped.
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https://hal.inria.fr/hal-01091184
Contributor : Pierre Peterlongo <>
Submitted on : Thursday, December 4, 2014 - 5:59:09 PM
Last modification on : Wednesday, July 3, 2019 - 8:24:01 AM
Long-term archiving on : Monday, March 9, 2015 - 6:00:29 AM

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  • HAL Id : hal-01091184, version 1

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Susete Alves Carvalho, Raluca Uricaru, Jorge Duarte, Claire Lemaitre, Nathalie Rivière, et al.. Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome. ECCB 2014, Sep 2014, Strasbourg, France. ⟨hal-01091184⟩

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