SYNOPSIS

kmc_tools [global parameters] <operation> [operation parameters]

DESCRIPTION

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)

EXAMPLE

kmc_tools union db1 -ci3 db2 -ci5 -cx300 db1_union_db2 -ci10

AUTHOR

KMC was originally written by:

• Sebastian Deorowicz (

• Marek Kokot

• Szymon Grabowski

• Agnieszka Debudaj-Grabysz

COPYING

KMC is free software distributed under GNU GPL3 licence for academic, research, and commercial use.