Heterozygosity parameters running time

[uceleste]

Dear All,

I would like to carry out two assembly test with Canu using both the parameters sets for:

• "Smash haplotypes together" corOutCoverage=200 ovlErrorRate=0.15 obtErrorRate=0.15

• "Avoid collapsing the genome" corOutCoverage=200 correctedErrorRate=0.040 "batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50"

If I understood well, the error rate used for "Smash haplotypes together" is three-fold higher (15%) than the default (5%). This means that the time of the assembly process will likely be three-time longer? And the running time of the process "Avoid collapsing the genome" instead?

I'm not complaining about the running time of this fantastic assembler. I only need these "time estimates" for some future planning. Many thanks!

[skoren]

The smash haplotypes will definitely be slower, I would expect 8-10-fold not 3-fold. Honestly, I rarely use these parameters because of the runtime and because they still won't collapse large structural variations (basically anything like an inversion/etc where there is no reasonable way to call a consensus of the variants). There is one genome I can remember where the heterozygosity was localized and simple differences where we used these settings.

The avoid collapsing runtime should be comparable to or faster than the defaults.

[uceleste]

Perfect, thank you very much for the answer. I will definitely take this information into account. Anyway, Canu is really a great assembler. Keep it up!