1. New findings from our paper, "These are not the k-mers you are looking for"

    Earlier today, I posted our response to the reviewers' comments on our k-mer counting paper, "These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure.

    A side note -- I was wondering how many public examples there are of the whole paper submission …

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  2. Response to reviewers for paper, "These are not the k-mers you are looking for"

    A few months back, we received some reviews for our paper on k-mer counting with khmer. After many months, we (mostly Qingpeng Zhang, the first author) has finished revising the paper. Here is our response to reviewers.

    The latest (resubmitted) version of the paper is here, while the version the …

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  3. Why you shouldn't use digital normalization

    Over the last year, digital normalization has occupied an increasingly privileged position in sequence analysis: it's a lightweight way to achieve an assembly, one that is computationally cheaper than almost anything else you can do; our software works reasonably well in practice; sequencing data generation capacity is only increasing; and …

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