a versatile toolkit for k-mers with taxonomic information
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 65.OS | Arch | File, 中国镜像 | Download Count |
---|---|---|---|
Linux | 64-bit | unikmer_linux_amd64.tar.gz, 中国镜像 |
|
Linux | 64-bit | unikmer_linux_arm64.tar.gz, 中国镜像 |
|
macOS | 64-bit | unikmer_darwin_amd64.tar.gz, 中国镜像 |
|
macOS | 64-bit | unikmer_darwin_arm64.tar.gz, 中国镜像 |
|
Windows | 64-bit | unikmer_windows_amd64.exe.tar.gz, 中国镜像 |
Notes:
unikmer version
to check update !!!unikmer autocompletion
to update shell autocompletion script !!!genautocomplete
to autocompletion
.help
.-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.unikmer
: slightly speedup for computing LCA.unikmer rfilter:
-E/--equal-to
supports multiple values.-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.unikmer rfilter:
change handling of black list.unikmer count
: syncmer value changed.int64
to uint64
unikmer info
: fix recounting problem for unsorted kmers but with Number.unikmer
:
5.0
.unikmer
:
unikmer
, including unikmer db info/index/search
.unikmer count
: fix syncmer.unikmer dump
: new flag --hashed
.unikmer stats
to unikmer info
, and add new column description
.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.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.unikmer
:
-nocheck-file
for not checking binary file.unikmer db index
: constructing index from binary filesunikmer db info
: printing information of index fileunikmer db search
: searching sequence from index databaseunikmer rfilter
: change format of rank order file.unikmer inter/union
: speedup for single input file.unikmer concat
:
-t/--taxid
for assigning global taxid, this can slightly reduce file size.-n/--number
for setting number of k-mers.unikmer num
:
-f/--force
for counting k-mers.unikmer locate
: output in BED6.unikmer locate/uniqs
: support multiple genome files.unikmer uniqs
:
-W/--seqs-in-a-file-as-one-genome
.unikmer count
:
-u/--unique
for output unique (single copy) kmersunikmer 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
:
unikmer count/diff/union
: slightly reduce memory and speedup when sorting k-mers.unikmer filter
: change scoring.