Kamil S. Jaron

I managed to develop an alternative plotting engine that avoids any of the problems with binning kmer pairs into fair squares. HOWEVER, that breaks the local agregation algorithm I wanted...

Solved in [b08e306](https://github.com/KamilSJaron/smudgeplot/commit/b08e306aab14b89c23cd426d62917c0c85711183)

Hi @shanku-li, in your case I would recommend to install the tool manually, not from conda (I don't know what is causing you this problem). Alternatively, you can use GitPod:...

What do you mean by synthetic? You mean by using Colchicine or something? What plant is it? The off 1n coverage estimates is one of the quirks of the older...

Imagine a diploid genome. Have two haplotypes C and D. Within this genome there is a paralogous region, the two copies are marked with * and ' ``` DDDDDDD'D'D'D'D*D*D*D*DDDDDD CCCCCCC'C'C'C'C*C*C*C*CCCCCC...

Normally I would recommend to increase k, which is something that reduces a lot of number of kmers in duplicates, while keeping the same number of heterozygous kmers (at least...

You have the right mindset! That's the way to think about these models... Your third attempt (of forcing the 10x) looks good, except there is something funny about the quantifications...

Hi @XiaoTW123, can you show the k-mer histogram? It would be helpful to diagnose the problem. If the genome is 5-7Gbp, it would explain a lot and you will be...

Hi, there is something going on with your run. It's either low coverage or very contaminated.... You can try to rerun GenomeScope with `-l 150` to see if that bump...

I should update the plot in the tutorial!!! Can you please past your plot without histograms here? We removed the histograms in the latest version because no one seems to...