simkaMin1

[main options]:

-in

(1 arg) : input file of datasets. One sample per line: id1: filename1...

-out

(1 arg) : output directory for result files (distance matrices) [Default: ./simka_results]

-seed

(1 arg) : seed used for random k-mer selection [Default: 100]

-bin

(1 arg) : path to simkaMinCore program (to be specified if not in PATH, or not in standard installation directory <simkaDir>/build/bin/simkaMinCore)

[core options]:

-nb-cores

(1 arg) : number of cores [Default: 0]

-max-memory

(1 arg) : max memory (MB) [Default: 8000]

[k-mer options]:

-kmer-size

(1 arg) : size of a kmer [Default: 21]

-nb-kmers

(1 arg) : number of kmers used to compute distances [Default: 1000000]

-filter

(0 arg) : filter out k-mer seen one time (potentially erroneous)

[read options]:

-max-reads

(1 arg) : maximum number of reads per sample to process [Default: 0]

-min-read-size

(1 arg) : minimal size a read should have to be kept [Default: 0]

-min-shannon-index

(1 arg) : minimal Shannon index a read should have to be kept. Float in [0,2] [Default: 0]