NAME

       kmds - control for population structure

DESCRIPTION

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

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

OPTIONS

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

       2) combine, and do metric multidimensional scaling with --mds_concat

   Required options:
       -k [ --kmers ] arg
              dsm kmer output file

       -p [ --pheno ] arg
              .pheno metadata

   MDS options:
       -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

   Filtering options:
       --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 --maf

   Other options:
       --version
              prints version and exits

       -h [ --help ]
              full help message

EXAMPLE

       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

AUTHOR

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