NAME¶

DESCRIPTION¶

-x

(0 arg) : radseq option, homogeneous read depth along the prediction

-predictions

(1 arg) : Input predictions

-reads

(1 arg) : Input reads

-unco

(1 arg) : Output uncoherent file name [default '/dev/null']

-co

(1 arg) : Output coherent file name

-hamming

(1 arg) : Maximal hamming distance authorized while maping [default '1']

-coverage_file (1 arg) :

File (.h5) generated by kissnp2, containing the coverage threshold per read set [default '_removemeplease']

-k

(1 arg) : Size of k, used as minial overlap and kmer spanning read coherence [default '31']

-index_stride

(1 arg) : Index Stride [default '2']

-size_seeds

(1 arg) : Size of the used seeds (distinct from the size of k) [default '25']

-output_fasta

(0 arg) : Output standard Fasta. By default the output is formatted especially for the discoSnp++ pipeline

-genotype

(0 arg) : Compute genotypes

-nb-cores

(1 arg) : number of cores [default '0']

-verbose

(1 arg) : verbosity level [default '1']

-version

(0 arg) : version

-help

(0 arg) : help

AUTHOR¶