---
name: "kmds"
section: "1"
platform: "linux"
package: "seer"
version: "1.1.4-8+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kmds"
---

# kmds(1)

control for population structure

## 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)](/seer/1.md) (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.