kmc_tools-filter - Online in the Cloud

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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