Is it better to Kmer count the combined fastq or the parts?

[mahesh-panchal]

Currently workflow does k-mer counting on the individual fastqs from each bam, but then goes on to combine the fastq. Should k-mer counting be performed on the combined fastq or the parts?

[MartinPippel]

I can check this out. The last time it was super buggy - and the step of producing symmetric kmers for the smudge plot always failed. However, if its working it should be much faster.