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.
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.
DiscoSNP is available as a binary for immediate use on Linux and MacOSX platforms, with the following requirements:
|MacOS-X 10.9 or above.
(Intel 64bit processors)
|Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)
For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.
|DiscoSNP tool is fully written in C++.||Download|
DiscoSNP user guide and VCF Creator user guide are available from this page.
DiscoSNP binaries and source code are covered by the Affero GPL version 3 license.