kmc_tools-filter1
Filter out reads with too small number of k-mers
Usage
kmc_tools filter
<kmc_input_db>
[kmc_input_db_params]
<input_read_set>
[input_read_set_params]
<output_read_set>
[output_read_set_params]
Overview
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
Examples
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
Copying
KMC is a free software distributed under GNU GPL3 licence for academic, research, and commercial use.
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.