GLOBAL MODE

iKISS was adapted to propose a Global mode. Useful if you are interested on counts kmers contained on genes by genetic group/population.

If you active KMERS_MODULE and unactive the “outliers mode”, so not active PCADAPT and LFMM steps, iKISS calculate occurrences of presence and absence of kmers into the populations/groups given by user into the SAMPLES_FILE. If MAPPING and INTERSECT are also activated you can check occurrences found into chosen features (genes).

If you want to activate the global mode configurate iKISS such as :

WORKFLOW:
    # convert reads in kmers and computes a binary matrix
    KMERS_MODULE : true
    # structure genotype based in ancestry
    SNMF: false #or true
    # structure genotype based in pca
    PCADAPT : false
    # calculate association between genotype and phenotype
    LFMM : false
    # mapping of kmers over a genomic reference
    MAPPING_KMERS: true
    # assembly kmers outliers detected by pcadapt and lfmm
    ASSEMBLY_KMERS : false
    # intersect outliers position (directly kmers or contigs) and features in a gff
    INTERSECT : true

Note

If you are in global mode, it is also possible to run SNMF; it is not incompatible.