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New
#Smudgeplot v0.2.2 is out https://github.com/KamilSJaron/smudgeplot/releases/tag/v0.2.2 … This time it's vastly heroic work of@calcnerd76: - new improvements to 1n estimation for pentaploids and higher ploidy levels - new informative warnings when 1n estimate might be shaky - AAAAND
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In the very first
#smudgeplot we had no algorithm that would identify individual smudges. I manually set a haploid coverage to place the labels on the smudges. This is the most beautiful triploid I have seen (and you can be deadly sure that the coverage ~207x) pic.twitter.com/gAfFQx1el1
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My personal guess would be that it will be really difficult to separate haplotypes in autopolyploid (too little heterozygosity). A good start would probably be to guess ploidy, have you heard about
#smudgeplot ? https://github.com/tbenavi1/smudgeplot … -
A new version o
#smudgeplot is out. We - turned off default quantile filtering - improved a bit estimation of 1n coverage for cases where triploid smudge was not detected, but hexaploid was. https://github.com/tbenavi1/smudgeplot/releases/tag/v0.1.3 … -
Interesting to hear, I would guess that variant calling should be fair with this coverage. The problem I see with these methods is that they need a good (haploid!) reference which is sometimes hard to generate.
#smudgeplot ftw -
Hey, that's a really nice
#smudgeplot. We found quite often diploid genomes with "bright" AABB smudges, but having a bright AAB smudge is quite rare. Is it possible that the genome is triploid? Do you also have the kmer histogram (e.g. the genomescope plot)? -
1/ ended up when I realized how little time people can spend on soft development in science compared to commertial programs 2/ ended up when I started to work on
#smudgeplot and realized how useful is when people report problemsPrikaži ovu nit -
The best we came out with was to look for kmers that are similar to each other, because we expected that the 1n peak should have many kmers paired within the 1n peak. This idea was the very seed of
#smudgeplotPrikaži ovu nit -
RT mike_schatz "RT KamilSJaron: Alright, I think
#smudgeplot is ready for the first brave testers. 1. It's a pure python package now; so the installation is `python3 http://setup.py install` 2. We have a single interface; see `smudgeplot -h` fo… https://twitter.com/KamilSJaron/status/1104903320249032704 …"
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