kmc_tools1
Additional operations on k-mer databases
Usage
kmc_tools [global
parameters]
<operation>
[operation
parameters]
Overview
This command and its various subcomments implement a number of operations on KMC databases.
k-mers sets operations for 2 KMC databases
intersect
intersection of 2 k-mers sets
kmers_subtract
subtraction of 2 k-mers sets
counters_subtract
counters subtraction of 2 k-mer sets
union
union of 2 k-mers sets
operations for single kmc database
sort
sorts k-mers from database generated by KMC2.x
reduce
exclude too rare and too frequent k-mers
compact
remove counters (store only k-mers)
histogram
histogram of k-mers occurr ences
dump
dump k-mers and counters to text file
more complex operations:
complex
complex operations with a number of input databases
other operations:
filter
filter out reads with too small number of k-mers
Options
global parameters:
-t<value>
total number of threads (default: no. of CPU cores)
-
-v -
enable verbose mode (shows some information) (default: false)
-
-hp -
hide percentage progress (default: false)
Examples
kmc_tools union db1 -ci3 db2 -ci5 -cx300 db1_union_db2 -ci10
Copying
KMC is free software distributed under GNU GPL3 licence for academic, research, and commercial use.
History
- Debian 13 (Trixie): the text shown here
- Debian 12 (Bookworm)
- Debian 11 (Bullseye)
- Debian 10 (Buster)
- Debian 9 (Stretch)