I have Illumina whole genome paired end short sequence reads of length 150 bp. I want to design k-mer, apply de-novo assembly and identify the SNPs markers. My questions are
1. What sizes of k-mer I should design. Do I need to design k-mer from both sides.
2. Which software do you think better for de novo assembly of k-mer?
3. For SNP mining, what steps should I follow (consider, my whole genome sequence data is from wild plant and there is no perfect reference data).