Comments (3)
PavelVesely
commented on July 1, 2024
However, I noticed that from some reason, with k=18 it's approx 2x slower compared to k=31. Is there any reason for this?
Interesting. My guess is that this is because of the dBG structure (much more branching / disconnected for
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PavelVesely
commented on July 1, 2024
Would be interesting to see the number of simplitigs for
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karel-brinda
commented on July 1, 2024
This doesn’t explain. In case of ProphAsm 1 there was no such effect.
Also,we dont construct dbg explicitely so dbg topology should play no role.
Maybe an effect of deletions in khash? This could in theory explain that….
(If answers for previously deleted kmers are slow)
Should be reproducible with two pneumococcal genomes, while computing
intersection and both sym diffs
…On Thu, Mar 14, 2024 at 5:36 PM Pavel Vesely ***@***.***> wrote:
Would be interesting to see the number of simplitigs for $k=18$ and $k=31$.
Not sure what else could cause such a big difference...
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Related Issues (9)
- Step 1: Efficient computation from KmerCamel tailored to simplitigs
- Step 2: intersections & deletions; interface mimicked from ProphAsm 1
- Feature request: Support for k-mer frequencies
- Feature request: Parallelism HOT 2
- Feature request: Rolling hashing HOT 1
- Feature request: k-mer length >32 with `-large` version included HOT 2
- Feature request: Reduce memory requirements for each simplitig by printing the right extensions directly to output.
- Support for k-mer sizes > 64
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