UNIKMER(1)

📦
version 0.20.0 · 2 versions
  • 0.20.0 · debian bookworm, debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking (latest)
  • 0.18.8 · ubuntu jammy
, in debian bookworm, debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 UNIKMER(1) 💖

okay bestie, pull up a chair, because this is the toolkit for nucleic acid k-mer analysis and it's genuinely iconic 🧬✨

✨ NAME ✨

unikmer — Toolkit for nucleic acid k-mer analysis

🌸 DESCRIPTION 🌸

unikmer — Toolkit for k-mer with taxonomic information 💅

So basically: unikmer is a toolkit for nucleic acid k-mer analysis, and it gives you functions including set operation on k-mers, optionally with TaxIds, but without count information. no cap.

K-mers are either encoded (when k<=32) or hashed (any k you want, queen), into uint64, and then serialized in a binary file with the extension .unik. that's the whole vibe.

TaxIds can be assigned when counting k-mers from genome sequences, and LCA (Lowest Common Ancestor) is computed during set opertions — yes, including computing union, intersection, set difference, unique and repeated k-mers. the way it just... does all of that. 👑

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 a taxonomy file from, like, the NCBI Taxonomy database. Please extract "nodes.dmp", "names.dmp", "delnodes.dmp" and "merged.dmp" from the link below into ~/.unikmer/:

ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

...or honestly some other directory if that's more your thing, and later you can refer to it using flag --data-dir or environment variable UNIKMER_DB. iykyk. 💖

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, so all TaxIds should be in the range of [1, 4294967295]. do not test this. fr fr.

👑 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
💖 bestie, if you wanna know more about any single command, just run:
unikmer [command] --help

that's it, that's the whole thing, and it will tell you more information about a command. slay. ✨

and that's a wrap, my love 🌈 this was unikmer version 0.19.0, dated August 2022 — go forth and k-mer, you absolute main character 🫶💜

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