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kmc_tools-filter - Online in the Cloud

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

This is the command kmc_tools-filter 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-filter - filter out reads with too small number of k-mers

SYNOPSIS


kmc_tools filter <kmc_input_db> [kmc_input_db_params] <input_read_set>
[input_read_set_params] <output_read_set> [output_read_set_params]

DESCRIPTION


This command filters out reads with too small number of k-mers.

OPTIONS


For k-mers database there are additional parameters:

-ci<value>
exclude k-mers occurring less than <value> times

-cx<value>
exclude k-mers occurring more of than <value> times

For the input set of reads there are additional parameters:

-ci<value>
remove reads containing less k-mers than value. It can be integer or floating number
in range [0.0;1.0]

-ci<value>
remove reads containing more k-mers than value. It can be integer or floating number
in range [0.0;1.0]

-f<a/q>
input in FASTA format (-fa), FASTQ format (-fq); default: FASTQ

For the output set of reads there are additional parameters:

-f<a/q>
output in FASTA format (-fa), FASTQ format (-fq); default: same as input

EXAMPLE


kmc_tools filter kmc_db -ci3 input.fastq -ci0.5 -cx1.0 filtered.fastq
kmc_tools filter kmc_db input.fastq -ci10 -cx100 filtered.fastq

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