Jellyfish for Paired End Reads

Question

[hpalk42]

Hello, I am assembling a whole genome for my masters project. I am trying to run Jellyfish and GenomeScope to get some information about genome characteristics. The genome was sequenced with Illumina paired-end sequencing, so we have both R1 and R2 files. My question is, do the files need to be combined in order to run Jellyfish? If so, how should I go about this? I am just a little confused about which step in the assembly I should (if ever) merge the two .fastq files. Any help would be appreciated!

[GenoMax]

I am just a little confused about which step in the assembly I should (if ever) merge the two .fastq files.

What program are you planning to use to assemble this data? You should not need to merge the fastq files on input to the program but check the help for particular program you are planning to use.