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Detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, discoSnp ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, discoSnp requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
C++
License:
CeCILL version 2.1
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Pierre Peterlongo

Institution(s)

GenScale, INRIA Rennes Bretagne-Atlantique, IRISA, Rennes, France

  • (Uricaru et al., 2015) Reference-free detection of isolated SNPs. Nucleic acids research.
    PMID: 25404127
  • (Neuman et al., 2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in bioinformatics.
    PMID: 22707752

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