Outils pour utilisateurs

Outils du site


"Specific k-mers Identification"

SkIf2, a new implementation of SkIf, much faster and using less RAM is available : https://sourcesup.renater.fr/wiki/skif2/

SkIf is a comparative genomics tool that detect genomic regions (from SNPs to genomic islands) specifically associated to a group of organisms (defined by the user).

SkIf can be employed to extract a specific genomic region related to a trait of interest.

How does SkIf works ?

SkIf was developed in C ++ and sequence reading is done using Bio++ bpp-seq library.



SkIf with singularity

A small caveat



Galaxy installation


Romain Gaborieau, Sylvain Gaillard, Martial Briand

Logo : Pierre Lerebours

Citing SkIf

Briand M, Gaborieau R, Jacques MA et al. SkIf: a tool for rapid identification of genes or regulators of interest [version 1; not peer reviewed]. F1000Research 2016, 5:1593 (poster) (doi: 10.7490/f1000research.1112490.1)

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

start.txt · Dernière modification: 2021/07/06 14:54 par martial.briand@inrae.fr