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Question about Hifiasm algorithm
In the review article "Genome assembly in the telomere-to-telomere era", @lh3 and @richarddurbin have mentioned that:
When constructing an overlap graph, we discard a read contained in longer reads. This apparently straightforward step may lead to assembly gaps...To alleviate this problem, hifiasm tries to rescue a contained read if having the read would patch an assembly gap. This heuristic works in simple cases but is not always reliable.
Can you please give some intuition for why this method is not reliable? Is this method difficult to implement, or is there a fundamental issue with this approach? Knowing your insights would be helpful.
Thanks!