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@cmkobel
cmkobel
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Carl Mathias Kobel cmkobel

Bioinformatician MSc, PhD.

Organizations

@conda-forge@TheMEMOLab

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cmkobel/README.md
                                      🦠  🧫  🔬  👾  🧪  💉  ☣

Hello. I'm a bioinformatician working in microbial ecology. I have a focus on software engineering and holo-omics. I research the interaction between gut microbes and their hosts. I try to keep my pipelines lean and share my workflows here on github mostly to train myself to make my work portable and well documented. I largely follow people on github who are into microbiology and omic-integrative methods.

My opinion on holo-omics is that we need to do more fundamental research and basic bioinformatic tool sharpening before we can truly dive in and understand the holistic interactions in the holobiont super-organisms. That is why I am currently also focusing on developing basic stuff like annotation and pipeline tools.

🚀 My current flagship project is theCompareM2 genomes-to-report pipeline which has just been published on bioconda.

I'm looking for a postdoctoral fellowship position in Copenhagen or online from spring 2025. Let me know if you have a lead.

Check out my personal webpage athttps://cmkobel.github.io/ for more info. Have a nice day!

                                   🦾   🔬   💻   🔣   💾   🚲   🧬

PinnedLoading

  1. CompareM2CompareM2Public

    🦠📇 Microbial genomes-to-report pipeline

    Python 58 3

  2. KMA-Aarhus/pappenheimKMA-Aarhus/pappenheimPublic

    ⚔️🏰 Pipeline for sequencing of SARS-CoV-2 on local workstations with realtime (ONT) basecalling

    R 2

  3. bioconda/bioconda-recipesbioconda/bioconda-recipesPublic

    Conda recipes for the bioconda channel.

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  4. conda-forge/staged-recipesconda-forge/staged-recipesPublic

    A place to submit conda recipes before they become fully fledged conda-forge feedstocks

    Python 750 5.4k

  5. snakemake/snakemakesnakemake/snakemakePublic

    This is the development home of the workflow management system Snakemake. For general information, see

    Python 2.5k 603

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