Pipeline configuration file

Before to run iKISS, create and adapt the pipeline on the configfile.yaml.

ikiss create_config -c configfile.yaml

Three sections are described on the configfile.yaml file.

Data section

First, adapt the configfile.yaml file with the fastq path (FASTQ) and the outfile path (OUTPUT) in the DATA section.

DATA:
   FASTQ: './DATATEST/fastq'
   OUTPUT: './OUTPUT-KISS/'

Warning

if you are using illumina paired reads, you need rename reads SAMPLE_R1.fastq.gz and SAMPLE_R2.fastq.gz. For single reads use SAMPLE_R1.fastq.gz

Note

iKISS uses compressed and decompressed fastq files

Workflow section

Chose the iKISS steps using the section WORKFLOW and parameter it with the PARAMS sections.

In WORKFLOW section, several modes can be launched:

Tool	Description
KMERS_MODULE	Convert reads in kmers, filter them and create a format ready to use in population genomics
PCADAPT	Detects genetic markers (kmers) involved in biological adaptation and provides outlier detection based on Principal Component Analysis (PCA).
LFMM	Used by iKISS for testing correlations between kmers and environmental data.
SNMF	Optionally used to compute least-squares estimates of ancestry proportions and ancestral allelic frequencies.
MAPPING_KMERS	Optionally used to align kmers to a genomic reference (if a reference is available).
ASSEMBLY_KMERS	Optionally assembles significant kmers obtained by pcadapt or lfmm.
INTERSECT	Optionally calculates how many kmers (if MAPPING_KMERS is activated) or contigs (if ASSEMBLY_KMERS is activated) are found in FEATURES (gene by default).

Note

KMERS_MODULE step has to be activated by default.

Note

̀PCADAPT`,`̀LFMM`, SNMF, MAPPING or ASSEMBLY are optional. Active or deactivate these steps using true or false.

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

Params section

In the PARAMS section, parameters of tools can be modified and adapted.

Please check the documentation of module you are interested to parameter integrated tools.