PCADAPT

PCADAPT detects kmers involved in biological adaptation and provides outlier detection based on Principal Component Analysis (PCA)

PARAMS:
   PCADAPT:
      K : 2
      CORRECTION: 'FDR'
      ALPHA : 0.05

Type	Description	Default Value
K	number K of principal components	2
CORRECTION	kmers outliers are obtained using a Bonferonni, BH correction or a FDR model	Bonferonni
ALPHA	modify the alpha cutoff for outlier detection	0.01

Sample file is a tabulated file contains accession_id and group columns:

accession_id group
Clone12      2
Clone14      2
Clone16      2
Clone20      2
Clone2       1
Clone4       1
Clone8       1

Type	Description	Default Value
accession_id	contains exactly same name of samples in FASTQ
phenotype_value	contains sample group (ex. wild=1, cultivated=2)