I'm on a European trip that involves several plane flights accompanied by long airport stays, and I just used some of that time to do a bit of tedious coding on khmer.
The coding I did was to add proper exception handling to khmer's internal file loading routines (see the …
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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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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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A few months back, we submitted a paper, These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure, to PLoS One. We got the (signed) reviews back in December, and I asked the reviewers if I could post their reviews publicly. They …
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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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We've just posted a new paper to arXiv: "These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure." We'll be submitting it to PLoS One after we wait a few days for comments from the Twittersphere and/or on Haldane's Sieve.
The …
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