kmds - control for population structure

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

kmds 1.1.2                                         March 2017                                            KMDS(1)

       Control for population structure.  Filter kmers and create a matrix representing population structure.

       This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).

       Filter kmers and create a matrix representing population structure with kmds

              kmds -k dsm_input.txt.gz --pheno metadata.pheno -o filtered

       To spread this process out, run the following command on each dsm file

              kmds -k dsm_input.txt.gz --pheno metadata.pheno --no_mds --size 10000

       kmds - control for population structure

       1) filter and subsample with --no_mds and --size

       2) combine, and do metric multidimensional scaling with --mds_concatRequiredoptions:-k [ --kmers ] arg
              dsm kmer output file

       -p [ --pheno ] arg
              .pheno metadata

   MDSoptions:-o [ --output ] arg
              output prefix for new dsm file

       --no_mds
              do not perform MDS; output subsampled matrix instead

       --write_distances
              write csv of distance matrix

       --mds_concat arg
              list of subsampled matrices to use in MDS. Performs only MDS; implies --no_filtering--pc arg (=3)
              number of principal coordinates to output

       --size arg (=1000000)
              number of kmers to use in MDS

       --threads arg (=1)
              number of threads. Suggested: 4

   Filteringoptions:--no_filtering
              turn off all filtering and do not output new kmer file

       --max_length arg (=100)
              maximum kmer length

       --maf arg (=0.01)
              minimum kmer frequency

       --min_words arg
              minimum kmer occurrences. Overrides --mafOtheroptions:--version
              prints version and exits

       -h [ --help ]
              full help message