Download

unikmer is implemented in Go programming language, statically-linked executable binary files are freely available.

Current Version

v0.20.0 - 2023-11-11

• unikmer:
  • update help messages
  • rename subcommand uniqs to map.
  • do not add the extension .unik if the value of flag -o/--out-prefix already has one.
• unikmer sort:
  • fix the bug of using both -d/--repeated and -m/--chunk-size, which seems to existed for 4 years.
• unikmer merge:
  • fix the bug of missing one record when taxid information is contained.
• unikmer num:
  • -f/--force also support sorted files.
• unikmer map:
  • fix a bug of missing some regions.
• unikmer locate:
  • fix seq ID error in output.
  • deduplicate output.

Links

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	unikmer_linux_amd64.tar.gz, 中国镜像
Linux	arm64	unikmer_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	unikmer_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	unikmer_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	unikmer_windows_amd64.exe.tar.gz, 中国镜像

Notes:

• please open an issue to request binaries for other platforms.
• run unikmer version to check update !!!
• run unikmer autocompletion to update shell autocompletion script !!!

Installation

Method 1: Install using conda

conda install -c bioconda unikmer

Method 2: Download binaries

Download the compressed executable file of your operating system, and decompress it with tar -zxvf *.tar.gz command or other tools. And then:

• For Linux-like systems

  • If you have root privilege, simply copy it to /usr/local/bin:

    sudo cp unikmer /usr/local/bin/
    

  • Or copy to anywhere in the environment variable PATH:

    mkdir -p $HOME/bin/; cp unikmer $HOME/bin/
    

• For Windows, just copy unikmer.exe to C:\WINDOWS\system32.

Method 3: Compile from source

1. Install go

   wget https://go.dev/dl/go1.17.13.linux-amd64.tar.gz
   
   tar -zxf go1.17.13.linux-amd64.tar.gz -C $HOME/
   
   # or
   #   echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc
   #   source ~/.bashrc
   export PATH=$PATH:$HOME/go/bin
   

2. Compile KMCP

   # ------------- the latest stable version -------------
   
   go get -v -u github.com/shenwei356/unikmer/unikmer
   
   # The executable binary file is located in:
   #   ~/go/bin/unikmer
   # You can also move it to anywhere in the $PATH
   mkdir -p $HOME/bin
   cp ~/go/bin/unikmer $HOME/bin/
   
   # --------------- the development version --------------
   
   git clone https://github.com/shenwei356/unikmer
   cd unikmer/unikmer/
   go build
   
   # The executable binary file is located in:
   #   ./unikmer
   # You can also move it to anywhere in the $PATH
   mkdir -p $HOME/bin
   cp ./unikmer $HOME/bin/
   

Shell-completion

Supported shell: bash|zsh|fish|powershell

Bash:

# generate completion shell
unikmer autocompletion --shell bash

# configure if never did.
# install bash-completion if the "complete" command is not found.
echo "for bcfile in ~/.bash_completion.d/* ; do source \$bcfile; done" >> ~/.bash_completion
echo "source ~/.bash_completion" >> ~/.bashrc

Zsh:

# generate completion shell
unikmer autocompletion --shell zsh --file ~/.zfunc/_unikmer

# configure if never did
echo 'fpath=( ~/.zfunc "${fpath[@]}" )' >> ~/.zshrc
echo "autoload -U compinit; compinit" >> ~/.zshrc

fish:

unikmer autocompletion --shell fish --file ~/.config/fish/completions/unikmer.fish

Release History

v0.19.1 - 2022-12-26

• unikmer: When environment variable UNIKMER_DB is set, explicitly setting --data-dir will overide the value of UNIKMER_DB.
• unikmer uniqs: skip sequences shorter than K.
• unikmer count/encode: limit the maximum k-mer size to 64.

v0.19.0 - 2022-04-25

• rename command genautocomplete to autocompletion.
• remove command help.
• change default value of option -j from 2 to 4.
• unikmer count/uniqs/locate: new flag -B/--seq-name-filter for filtering out unwanted sequences like plasmids.
• unikmer count: add support of .xz and .zst files.

v0.18.8 - 2021-09-17

• use new version of nthash with better performance.
• unikmer info: fix typoes.

v0.18.7 - 2021-08-30

• unikmer: better counting speed by upstream optimization of FASTA/Q parsing.
• unikmer concat: fix parsing flag -n.

v0.17.3 - 2021-05-16

• unikmer: fix buiding for 386. #21

v0.17.2 - 2021-02-05

• unikmer: slightly speedup for computing LCA.
• unikmer rfilter:
  • flag -E/--equal-to supports multiple values.
  • new flag -n/--save-predictable-norank: do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff.

v0.17.1 - 2021-01-18

• unikmer rfilter: change handling of black list.

v0.17.0 - 2021-01-15

• syncmer value changed with different hash method.
• unikmer count: syncmer value changed.

v0.16.1 - 2020-12-28

• change Header.Number from int64 to uint64
• unikmer info: fix recounting problem for unsorted kmers but with Number.

v0.16.0 - 2020-12-28

• unikmer:
  • binary file format change: fix reading long description, and bump version to 5.0.
  • better binary file parsing performance.

v0.15.0 - 2020-12-25

• unikmer:
  • binary file minor change: increase description maximal length from 128 B to 1KB.
  • separating k-mers (sketches) indexing and searching from unikmer, including unikmer db info/index/search.
• unikmer count: fix syncmer.
• unikmer dump: new flag --hashed.
• rename unikmer stats to unikmer info, and add new column description.

v0.14.0 - 2020-11-25

• unikmer union: fix bug when flag -s not given.
• unikmer count/uniqs/locate: performance improvement on generating k-mers.
• unikmer count/db: support scaled/minizimer/syncmer sketch.
• unikmer stats: change format.

v0.13.0 - 2020-10-23

• new command unikmer common: Finding k-mers shared by most of multiple binary files.
• unikmer common/count/diff/grep/rfilter/sort/split/union: faster sorting.
• unikmer uniqs: better result for flag --circular.
• unikmer search: fix a bug when searching on database with more than one hash.

v0.12.0 - 2020-09-24

• unikmer:
  • support longer k (k>32) by saving ntHash.
  • new flag -nocheck-file for not checking binary file.
• new commands:
  • unikmer db index: constructing index from binary files
  • unikmer db info: printing information of index file
  • unikmer db search: searching sequence from index database
• unikmer rfilter: change format of rank order file.
• unikmer inter/union: speedup for single input file.
• unikmer concat:
  • new flag -t/--taxid for assigning global taxid, this can slightly reduce file size.
  • new flag -n/--number for setting number of k-mers.
• unikmer num:
  • new flag -f/--force for counting k-mers.
• unikmer locate: output in BED6.
• unikmer locate/uniqs: support multiple genome files.
• unikmer uniqs:
  • stricter multiple mapping limit.
  • new flag -W/--seqs-in-a-file-as-one-genome.
• unikmer count:
  • new flag -u/--unique for output unique (single copy) kmers

v0.11.0 - 2020-07-06

• new command: unikmer rfilter for filtering k-mers by taxonomic rank.
• unikmer inter: new flag -m/--mix-taxid allowing part of files being whithout taxids.
• unikmer dump: fix a nil pointer bug.
• unikmer count:
  • fix checking taxid in sequence header.
  • fix setting global taxid.
• unikmer count/diff/union: slightly reduce memory and speedup when sorting k-mers.
• unikmer filter: change scoring.
• unikmer count/locate/uniqs: remove flag --circular.

v0.10.0 - 2020-05-21

• unikmer: fix loading custom taxonomy files.
• unikmer count:
  • new flag -d for only count duplicate k-mers, for removing singleton in FASTQ.
  • fix nil pointer bug of -t.
• unikmer split: fix memery and last odd k-mer mising bug for given ONE sorted input file.
• unikmer sort: skip loading taxonomy data when neither -u or -d given.
• unikmer diff: 2X speedup, and requiring 1th file being sorted.
• unikmer inter: 2-5X speedup, and requiring all files being sorted, sorted output by default.

v0.9.0 - 2020-02-18

• unikmer: new binary format supporting optional Taxids.
• deleted command: unikmer subset.
• new command: unikmer head for extracting the first N k-mers.
• new command: unikmer tsplit for splitting k-mers according to taxid.
• unikmer grep: support searching with taxids.
• unikmer count: support parsing taxid from FASTA/Q header.

v0.8.0 - 2019-02-09

• unikmer:
  • new option -i/--infile-list, if given, files in the list file are appended to files from cli arguments.
  • improve performance of binary file reading and writing.
• unikmer sort/split/merge: safer forcing deletion of existed outdir, and better log.
• unikmer split: performance improvement for single sorted input file.
• unikmer sort: performance improvement for using -m/--chunk-size.
• unikmer grep: rewrite, support loading queries from .unik files.
• unikmer dump: fix number information in output file.
• unikmer concat: new flag -s/--sorted.

v0.7.0 - 2019-09-29

• new command unikmer filter: filter low-complexity k-mers.
• new command unikmer split: split k-mers into sorted chunk files.
• new command unikmer merge: merge from sorted chunk files.
• unikmer view:
  • new option -N/--show-code-only for only showing encoded integers.
  • fix output error for -q/--fastq.
• unikmer uniqs:
  • new option -x/--max-cont-non-uniq-kmers for limiting max continuous non-unique k-mers.
  • new option -X/--max-num-cont-non-uniq-kmers for limiting max number of continuous non-unique k-mers.
  • fix bug for -m/--min-len.
• unikmer union:
  • new option -d/--repeated for only printing duplicate k-mers.
• unikmer sort:
  • new option -u/--unique for removing duplicate k-mers.
  • new option -d/--repeated for only printing duplicate k-mers.
  • new option -m/--chunk-size for limiting maximum memory for sorting.
• unikmer diff:
  • small speed improvements.

v0.6.2 - 2019-01-21

• unikmer encode: better output for bits presentation of encoded k-mers (-a/--all)

v0.6.1 - 2019-01-21

• unikmer dump:
  • new option -K/--canonical to keep the canonical k-mers.
  • new option -k/--canonical-only to only keep the canonical k-mers.
  • new option -s/--sorted to save sorted k-mers.
• unikmer encode: add option -K/--canonical to keep the canonical k-mers.

v0.6.0 - 2019-01-20

• unikmer: check encoded integer overflow
• new command unikmer encode: encode plain k-mer text to integer
• new command unikmer decode: decode encoded integer to k-mer text

v0.5.3 - 2018-11-28

• unikmer count/dump: check file before handling them.

v0.5.2 - 2018-11-28

• unikmer locate: fix bug.
• unikmer: doc update.

v0.5.1 - 2018-11-07

• unikmer locate/uniqs: fix options checking.

v0.5.0 - 2018-11-07

• unikmer diff: fix concurrency bug when cloning kmers from first file.
• new command unikmer locate: locate Kmers in genome.
• new command unikmer uniqs: mapping Kmers back to genome and find unique subsequences.

v0.4.4 - 2018-10-27

• unikmer: add global option -L/--compression-level.
• unikmer diff: reduce memory occupation, speed not affected.

v0.4.3 - 2018-10-13

• unikmer diff: fix bug of hanging when the first file having no Kmers.

v0.4.2 - 2018-10-13

• unikmer stats/diff: more intuitional output

v0.4.1 - 2018-10-10

• Better performance of writing and reading binary files

v0.4.0 - 2018-10-09

• Binary serialization format changed.
• new command unikmer sort: sort binary files
• unikmer count/diff/union/inter: better performance, add option to sort Kmers which significantly reduces file size
• unikmer dump: changed option
• unikmer count: changed option

v0.3.1 - 2018-09-25

• Binary serialization format changed.
• new command unikmer stats: statistics of binary files.
• unikmer: adding global option -i/--infile-list for reading files listed in file.
• unikmer diff: fixed a concurrency bug when no diff found.

v0.2.1 - 2018-09-23

• unikmer count: performance improvement and new option --canonical for only keeping canonical Kmers.

v0.2.0 - 2018-09-09

• new command unikmer sample: sample Kmers from binary files.
• new global options:
• -c, --compact: write more compact binary file with little loss of speed.
• -C, --no-compress: do not compress binary file (not recommended).
• some improvements.

v0.1.0 - 2018-08-09

• first release