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kmc_tools - Online in the Cloud

Run kmc_tools in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command kmc_tools that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


kmc_tools - additional operations on k-mer databases

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

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