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

# seer(1)

sequence element enrichment analysis

## NAME

seer - sequence element enrichment analysis

## DESCRIPTION

Sequence Element Enrichment Analysis

The .pheno file format is tab separated, two columns with sample name, one with phenotype. Phenotypes of only 0 or 1 will be treated as binary, any other value and the phenotype will be treated as quantitative. Therefore for missing phenotype values the sample should simply be excluded from this file.

## OPTIONS

### Required options:

- **-k** \[ **--kmers** \] arg

  dsm kmer output file

- **-p** \[ **--pheno** \] arg

  .pheno metadata

### Covariate options:

- **--struct** arg

  mds values from kmds

- **--covar\_file** arg

  file containing covariates

- **--covar\_list** arg

  list of columns covariates to use. Format is 1,2q,3 (use q for quantitative)

### Performance options:

- **--threads** arg (=1)

  number of threads. Suggested: 4

### Filtering options:

- **--no\_filtering**

  turn off all filtering and peform tests on all kmers input

- **--max\_length** arg (=100)

  maximum kmer length

- **--maf** arg (=0.01)

  minimum kmer frequency

- **--min\_words** arg

  minimum kmer occurrences. Overrides **--maf**

- **--chisq** arg (=10e-5)

  p-value threshold for initial chi squared test. Set to 1 to show all

- **--pval** arg (=10e-8)

  p-value threshold for final logistic test. Set to 1 to show all

### Other options:

- **--print\_samples**

  print lists of samples significant kmers were found in

- **--version**

  prints version and exits

- **-h** \[ **--help** \]

  full help message

## EXAMPLES

Basic usage:

-

  seer -k dsm\_input.txt.gz --pheno metadata.pheno \> significant\_kmers.txt

To use the kmds output, increase execution speed and give the most complete output

-

  seer -k filtered.gz --pheno metadata.pheno --struct filtered.dsm --threads 4 --print\_samples

## AUTHOR

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