DOKK / manpages / debian 12 / seer / kmds.1.en
KMDS(1) User Commands KMDS(1)

kmds - control for population structure

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

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

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

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

dsm kmer output file
.pheno metadata

output prefix for new dsm file
do not perform MDS; output subsampled matrix instead
write csv of distance matrix
list of subsampled matrices to use in MDS. Performs only MDS; implies --no_filtering
number of principal coordinates to output
number of kmers to use in MDS
number of threads. Suggested: 4

turn off all filtering and do not output new kmer file
maximum kmer length
minimum kmer frequency
minimum kmer occurrences. Overrides --maf

prints version and exits
full help message

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

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

March 2017 kmds 1.1.2