| KMC_TOOLS-INTERSECT(1) | KMC_TOOLS-INTERSECT(1) |
NAME¶
kmc_tools-intersect - calculate intersection of two KMC databases
SYNOPSIS¶
kmc_tools intersect <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
DESCRIPTION¶
The output database will contain only k-mers that are present in both input sets. The counter value in the output database is equal to the lower counter value in the input.
OPTIONS¶
For each input 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 output 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
-cs<value>
maximal value of a counter
EXAMPLE¶
kmc -k28 file1.fastq kmers1 tmp kmc -k28 file2.fastq kmers2 tmp kmc_tools intersect kmers1 -ci10 -cx200 kmers2 -ci4 -cx100 kmers1_kmers2_intersect -ci20 -cx150
AUTHOR¶
KMC was originally written by:
•Sebastian Deorowicz (
<sebastian.deorowicz@polsl.pl>)
•Marek Kokot
•Szymon Grabowski
•Agnieszka Debudaj-Grabysz
COPYING¶
KMC is a free software distributed under GNU GPL3 licence for academic, research, and commercial use.