Kamil S. Jaron

add the information about the error line: L + cov vs L / cov line

Hi, thanks for posting. This genome indeed looks very funky. I think some of the smudges are a noise due to low L and coverage (the one that is on...

(problem with data) 2 species, one octoploid, one diploid were mixed together (I accidentally pulled a wrong library from ncbi) 


Hi Cyril, I am glad to see you work on freaky stuff now :-) (223e6 * 300) / 45e6 = 1486.667 (here 45e6 is the genome size). That's a psycho...

Cool, we are getting somewhere. We see the most of the kmer pairs still up, but it does look much nicer than before (it's not railing the top edge). The...

@RNieuwenhuis yep, we did experiment with using only kmers differing in the middle nt. The implementation of the middle position kmer pair search was successful (fast and without too high...

@RNieuwenhuis you also wrote > Also, can you indicate in the README and/or wiki what are the differences between the het_kmers and smudge_pairs? I am running smudge_pairs for a month...

Ouch, that's a massive genome. I completely see why it might take so long. To be honest, I am right now a bit buried in other obligations and I won't...

Excellent! I think the most reasonable would be to write first a pythonic version. Even if it should be just a prototype for a KMC based version. I think it's...