SkIf2 is a comparative genomic tool that detect genomic regions (from SNPs to genomic islands) specifically associated to a group of organisms (defined by the user).
SkIf2 can be employed to extract a specific genomic region related to a trait of interest.
SkIf2 is a new implementation of SkIf (Specific k-mers Identification, https://sourcesup.renater.fr/wiki/skif/).
SkIf2 allows to obtain 100% identical results to SkIf much faster and using less RAM, then SkIf2 can be used on hundreds or thousands of genomes.
SkIf2 was developed in C++ and is a software tool relying on GATB-CORE library.(https://gatb.inria.fr/software/gatb-core/)

Dependencies : cmake 2.8+ should be already installed (mandatory).

git clone https://git.renater.fr/anonscm/git/skif2/skif2.git
cd skif2
mkdir build
cd build
cmake ..
make -j8

SkIf2 -inGroupFile inGroupGenomePathsFile.txt -outGroupFile outGroupGenomePathsFile.txt -k 15 -outputPrefix specificInGroupKmers

Example

License

SkIf2 with singularity

Martial Briand.

Denancé N, Briand M, Gaborieau R, Gaillard S and Jacques MA. Identification of genetic relationships and subspecies signatures in Xylella fastidiosa. BMC Genomics, 2019, 20:239. (doi: https://doi.org/10.1186/s12864-019-5565-9)

Contact : martial DOT briand AT inra DOT fr