Question: K-mer size and de-novo assembly and SNP mining
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gravatar for ram.mainali
2.7 years ago by
ram.mainali20
ram.mainali20 wrote:

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).

ADD COMMENTlink modified 2.7 years ago by WouterDeCoster43k • written 2.7 years ago by ram.mainali20
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