---
name: "unikmer"
section: "1"
platform: "linux"
package: "unikmer"
version: "0.20.0-1+b9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/unikmer"
---

# unikmer(1)

Toolkit for nucleic acid k-mer analysis

## NAME

unikmer - Toolkit for nucleic acid k-mer analysis

## DESCRIPTION

unikmer - Toolkit for k-mer with taxonomic information

unikmer is a toolkit for nucleic acid k-mer analysis, providing functions including set operation on k-mers optional with TaxIds but without count information.

K-mers are either encoded (k\<=32) or hashed (arbitrary k) into 'uint64', and serialized in binary file with extension '.unik'.

TaxIds can be assigned when counting k-mers from genome sequences, and LCA (Lowest Common Ancestor) is computed during set opertions including computing union, intersection, set difference, unique and repeated k-mers.

Version: v0.19.0

Author: Wei Shen \<shenwei356@gmail.com\>

Documents  : https://bioinf.shenwei.me/unikmer Source code: https://github.com/shenwei356/unikmer

Dataset (optional):

-

  Manipulating k-mers with TaxIds needs taxonomy file from e.g., NCBI Taxonomy database, please extract "nodes.dmp", "names.dmp", "delnodes.dmp" and "merged.dmp" from link below into ~/.unikmer/ , ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz , or some other directory, and later you can refer to using flag **--data-dir** or environment variable UNIKMER\_DB.

-

  For GTDB, use 'taxonkit create-taxdump' to create NCBI-style taxonomy dump files, or download from:

-

  https://github.com/shenwei356/gtdb-taxonomy

-

  Note that TaxIds are represented using uint32 and stored in 4 or less bytes, all TaxIds should be in the range of \[1, 4294967295\]

### Usage:

-

  unikmer \[command\]

### Available Commands:

-

  autocompletion Generate shell autocompletion script (bash\|zsh\|fish\|powershell) common         Find k-mers shared by most of multiple binary files concat         Concatenate multiple binary files without removing duplicates count          Generate k-mers (sketch) from FASTA/Q sequences decode         Decode encoded integer to k-mer text diff           Set difference of multiple binary files dump           Convert plain k-mer text to binary format encode         Encode plain k-mer text to integer filter         Filter out low-complexity k-mers (experimental) grep           Search k-mers from binary files head           Extract the first N k-mers info           Information of binary files inter          Intersection of multiple binary files locate         Locate k-mers in genome merge          Merge k-mers from sorted chunk files num            Quickly inspect number of k-mers in binary files rfilter        Filter k-mers by taxonomic rank sample         Sample k-mers from binary files sort           Sort k-mers in binary files to reduce file size split          Split k-mers into sorted chunk files tsplit         Split k-mers according to taxid union          Union of multiple binary files uniqs          Mapping k-mers back to genome and find unique subsequences version        Print version information and check for update view           Read and output binary format to plain text

### Flags:

- **-c**, **--compact**

  write compact binary file with little loss of speed

- **--compression-level** int

  compression level (default **-1**)

- **--data-dir** string

  directory containing NCBI Taxonomy files, including nodes.dmp, names.dmp, merged.dmp and delnodes.dmp (default "/home/nilesh/.unikmer")

- **-h**, **--help**

  help for unikmer

- **-I**, **--ignore-taxid**

  ignore taxonomy information

- **-i**, **--infile-list** string

  file of input files list (one file per line), if given, they are appended to files from cli arguments

- **--max-taxid** uint32

  for smaller TaxIds, we can use less space to store TaxIds. default value is 1\<\<32-1, that's enough for NCBI Taxonomy TaxIds (default 4294967295)

- **-C**, **--no-compress**

  do not compress binary file (not recommended)

- **--nocheck-file**

  do not check binary file, when using process substitution or named pipe

- **-j**, **--threads** int

  number of CPUs to use (default 4)

- **--verbose**

  print verbose information

Use "unikmer \[command\] **--help**" for more information about a command.