Canu possibly idling in the "meryl" step
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20 months ago
Macspider ★ 3.6k


I'm doing metagenomic pacbio data assembly using canu. I have tried a few runs with different parameters to see what N50 I would get and estimate a good k-mer size.

Each run has lasted for approx. 3-4 hours, as long as the set k-mer size was below 50. In the last run I have brought the k-mer size to 101 and it has been going on for what are now 4 days and it still is at the "meryl" step, which I suppose is where it counts k-mers and their occurrences.

Now, I know that assemblies take long but could it be that canu is for some reason idling at the meryl step? Did anybody experience this in their work already?

canu meryl assembly genomics kmer • 409 views

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