I want to know how hgap select the seed. The paper says it selects the seed with more than 20x coverage, but doesn't say how it counts the coverage.
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Originally posted by Rui Guo View PostDo that mean the automatically selected seeds are long enough and has enough coverage? Does it calculate kmer frequency?
As rhall stated, When you set up the run, you input a Genome Size (bp). The algorithm will sort the subreads by length, compute the quantity of bases necessary to obtain appropriate coverage for the Genome Size (bp) that you input during setup and select the longest data necessary to obtain the 30X coverage.
See this for more details:
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