| KMC_TOOLS-FILTER(1) | KMC_TOOLS-FILTER(1) |
NAME¶
kmc_tools-filter - filter out reads with too small number of k-mersSYNOPSIS¶
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
AUTHOR¶
KMC was originally written by:•Sebastian Deorowicz (
<sebastian.deorowicz@polsl.pl>)
•Marek Kokot
•Szymon Grabowski
•Agnieszka Debudaj-Grabysz