Moritz Buck

Microbes of all sorts, mainly aquatic, but open to all biomes. That is what I use my bioinformatics for. Also posting baby stuff now apparently, for some reaso

[Moritz Buck @MetaMoritz]

Where you ever sad that you could not compute core-genomes for this collection of incomplete [MS]AGs you had lying around? Or simply to throw away a lot of data by dereplicating? I coded a thing: https://t.co/R2ZgxDHUjc with @mehrshmali and @Stebe69 1/4

[Moritz Buck @MetaMoritz]

@fesshole Weaponized incompetence is a thing....

[Moritz Buck @MetaMoritz]

@nomad421 Brewing....

[Moritz Buck @MetaMoritz]

@mehrshmali @_SLU Did you also post the "one day later" pic? :P

[Maliheh Mehrshad @mehrshmali]

Apply to this long-term #postdoc position!

Come and join us in our marvelous path towards understanding the role of phage co-infection in their genome evolution and become a member of the *MULTIPHAGE* #ERCStG team!

Please retweet or is it reX now😉

https://t.co/hSwgVKZdtS

[Moritz Buck @MetaMoritz]

Pandoc, bless your soul.

[Moritz Buck @MetaMoritz]

Combinatorial sequence analysis: try the forward, then the reverse, and the rev-comp, and then repeat with R2, pick whatever matches most....

[Moritz Buck @MetaMoritz]

@miangoar Nah, dumber, the static layout is just based on a graph where the edges connect all genomes that have an ANI > 91.5 (slightly arbitrary, to have a reasonable picture)

[Moritz Buck @MetaMoritz]

Stuck in a species clustering rabbit hole: Pelagibacterales' ANI gap (edges ANI > 91.5%)

[Moritz Buck @MetaMoritz]

@K_T_Jurdzinski Well, I can't get convinced by the recombination barrier until we find a species that doesn't recombine... Anyhow, the same threshold doesn't work for some pelagi' species (they still have a barrier though) which lead me to this rabbit hole...

[Moritz Buck @MetaMoritz]

@K_T_Jurdzinski There is no real dimensionality reduction, it's just a standard fruchterman-reingold graph layout ^^

[Moritz Buck @MetaMoritz]

@naturepoker1 @biomonika In all fairness i imagine some manual copypasta scaffolding

[Moritz Buck @MetaMoritz]

@naturepoker1 @biomonika Then the line would be exactly twice as long though..... I would blame sequence pixies!

[Moritz Buck @MetaMoritz]

@naturepoker1 @biomonika Well then i would hope the second file starts with a new entry and at least I'd see a "greater than" lost in the middle of it... Uhhh all the dirty scenarios i have in my mind now....

[Moritz Buck @MetaMoritz]

@m_chuvochina @AlexJProbst All smoke mirrors and more, won't doesn't matter if on 3 years postdoc you have 5 contracts, got asked to quit because the money moved faculty and told after 2.5 years grant hasn't enough money because you're not allowed to consider obligatory salary increases... #BitterPostDoc

[Moritz Buck @MetaMoritz]

@AlexJProbst @ISMEJournal @FEMSmicro I replied anyhow, but i know the story it comes out of and i think it's easy to misconstrue some aspects of this discussion without enough context.....

[Moritz Buck @MetaMoritz]

@AlexJProbst @ISMEJournal @FEMSmicro I do have to complain, the whole first page of questions already assumes i accept data embargoes.... Makes it difficult for me to answer without making it look like i stand behind that practice... Also, it's very black and white...

[Moritz Buck @MetaMoritz]

New amplicon misnomer: "Precision Metagenomics"

[Moritz Buck @MetaMoritz]

@BioMickWatson @Njuki_Sue @s_jaenicke All of that. But if NCBI not there the NCBI taxonomy interface of biopython can do the job, or taxize for R.

[Moritz Buck @MetaMoritz]

@BioMickWatson @npcooley The restful API is weirdly useable, between the KO entries and the ORG entries can get some info there, and can be done with `wget` and bash. But wouldn't trust it to much... It would be buased on validated stuff. I would probably run kofamscan against nr or something

[Moritz Buck @MetaMoritz]

@knstnr Fast so gut wie Tatort! ;)