| Linux | Mac OSX |
|---|---|
DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, 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.
Uricaru R., Rizk G., Lacroix V., Quillery E., Plantard O., Chikhi R., Lemaitre C., Peterlongo P. (2014). Reference-free detection of isolated SNPs. Nucleic Acids Research 43(2):e11.
Peterlongo, P., Riou, C., Drezen, E., Lemaitre, C. (2017). DiscoSnp ++ : de novo detection of small variants from raw unassembled read set(s). BioRxiv.
Gauthier, J., Mouden, C., Suchan, T., Alvarez, N., Arrigo, N., Riou, C., Lemaitre, C., Peterlongo, P. (2017). DiscoSnp-RAD: de novo detection of small variants for population genomics. BioRxiv
We propose a DiscoSnp++ adaptation for RAD-Seq data. A script, called run_discoSnpRad.sh, is adapted to this kind of data. See below for more details.
CMake 2.6+; see http://www.cmake.org/cmake/resources/software.html
c++ compiler; compilation was tested with gcc and g++ version>=4.5 (Linux) and clang version>=4.1 (Mac OSX).
# get a local copy of DiscoSnp source code
git clone --recursive https://github.com/GATB/DiscoSnp.git
# compile the code an run a simple test on your computer
cd DiscoSnp
sh INSTALL# create the conda environment
conda create -p discoSnp_env discoSnp
# activate the create environment
conda activate discoSnp_envOnce activated, scripts run_discoSnp++.sh and run_discoSnpRad.sh are executable.
Binary release for Linux and Mac OSX are provided within the "Releases" tab on Github/DiscoSnp web page.
After downloading and extracting the content of the binary archive, please run the following command from DiscoSnp home directory:
chmod +x run_discoSnp++.sh test/*.sh scripts/*.sh
Run DiscoSnp WITHOUT mapping results on a reference genome:
./run_discoSnp++.sh -r test/fof.txt -T
Run DiscoSnp WITH mapping results on a reference genome (requires bwa):
./run_discoSnp++.sh -r test/fof.txt -T -G test/reference_genome.fa
Note: if bwa is not in you PATH, then add the option "-B path_to_bwa". For instance:
./run_discoSnp++.sh -r test/fof.txt -T -G test/reference_genome.fa -B /home/me/my_programs/bwa-0.7.12/
Run DiscoSnp WITH mapping results on a reference genome AND using this reference genome for calling variants:
./run_discoSnp++.sh -r test/fof.txt -T -G test/reference_genome.fa -R
See doc/discoSnp_user_guide.pdf or doc/discoSnp_user_guide.txt
While dealing with RAD-Seq data, run_discoSnpRad.sh script should be used. It uses options specific to RAD-Seq: branching strategy, kind of extensions, abundance threshold, and kind of bubbles to be found. Moreover, it clusters variants per locus by calling the discoRAD_finalization.sh pipeline. Cluster information is reported in the final provided VCF file.
A README file describes all scripts and the discoRAD_finalization.sh pipeline.
Remarks and questions: https://www.biostars.org/t/discosnp/
Contact: Pierre Peterlongo: [email protected]