I am completely new to Velvet, and I am mainly using "Vague" GUI to work with Velvet. I have been trying to experiment a lot with all the parameters, but now I wish to understand which parameters mainly are best suited for my dataset.
I have two .fq files, one being the first mates on the forward strand, and the other being the second mates on the reverse strand. Average length of both is 70bp. Outer distance between two pairs is around 500bp. I want to assembly the genomes and get the reference.
I wish to know if I am in the right track at all. What I am doing is that I am choosing a k-mer size of 31. Coverage cutoff and expected coverage and Minimum contig length are all set to Auto. Read type: paired end. Interleaved sequence file: separate.
The full task is here:
What does "assemble the other genome" refer to? The task in general is quite unclear to me.