kmc_tools-intersect1
Calculate intersection of two kmc databases
Usage
kmc_tools intersect
<input1
[input1_params]
>
<input2
[input2_params]
>
<output
[output_params]
>
Overview
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
Examples
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
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.