DiscoSNP

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads. The number of input read sets is not constrained, it can be one, two, or more. No reference genome is needed. DiscoSnp became DiscoSnp++, and can now detect all kinds of SNPs (not only isolated ones) and insertions and deletions.

Software discoSnp++ is designed for discovering Single Nucleotide Polymorphism (SNP) and insertions/deletions (indels) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
The outputs are fasta files containing variants and a VCF file using or not a reference genome.

Reference

Uricaru, Raluca; Rizk, Guillaume; Lacroix, Vincent; Quillery, Elsa; Plantard, Olivier; Chikhi, Rayan; Lemaitre, Claire; Peterlongo, Pierre. (2014). Reference-free detection of isolated SNPs. Nucleic Acids Research 43(2):e11.

Ready-to-use executable

DiscoSNP is available as a binary for immediate use on Linux and MacOSX platforms, with the following requirements:

maclogo MacOS-X 10.9 or above.
(Intel 64bit processors)
Download
linuxlogo Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)
Download

For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.

Source Code

cpp-logo DiscoSNP tool is fully written in C++. Download

Documentation

DiscoSNP user guide and VCF Creator user guide are available from this page.

License

DiscoSNP binaries and source code are covered by the Affero GPL version 3 license.

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