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discoSnp++ 

[page edited on June, 18, 2020] - github webpageScreen Shot 2015-03-25 at 11.47.06

Tutorial

A toturial can be followed from those slides demo_discosnp

Description

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 software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads2, enhance the kissnp2 results by computing per read set  and for each variant found  i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism.

A VCF file using or not a reference genome is also created.

Input (what about read pairs?)

discoSnp takes raw NGS datasets as inputs (fasta, fastq, gzipped or not). No reference genome is required. Read pairs can be given, however the pair information are useless in this framework. The detected SNPs are output in the contig they belong to and the contig length does not depend on pairing information. By the way, two reaf files correspond to paired reads should belong to the same file of files. (see documentations)

Short presentation:

Here are a few slides about discoSnp: colloque_GE_2013_discoSnp

Paper & Citation

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. doi:10.1093/nar/gku1187

C. Riou,  C. Lemaitre, and P. Peterlongo, “VCF_creator: Mapping and VCF Creation features in DiscoSnp++”. Poster at Jobim 2015

Forum

For remark and question, please use the biostar forum

Download

github page: https://github.com/GATB/DiscoSnp

Galaxy

  • discoSnp can be used on the GenOuest galaxy server
  • discoSnp can be integrated in your galaxy instance using the GenOuest Toolshed (section Symbiose or Next generation Sequencing)
    • directly via the toolshed (without authentification) by downloading the source code latest version (in zip, tar.gz or tar.bz2 format)
    • by adding the GenOuest toolshed in the “tool_sheds_conf.xml” file in your Galaxy configuration and by installing discoSnp within the Admin panel (Search and browse tool sheds)

Packages debian and ubuntu:

discoSnp is also available via debian and ubuntu

NAR Paper datasets

We believe that the datasets that were used for testing discoSnp may be useful for testing similar tools. All simulated datasets presented in the NAR paper are available from this web site.

n Coli datasets

Human dataset