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                                      🦠  🧫  🔬  👾  🧪  💉  ☣

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 the Assemblycomparator2 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.

                                   🦾   🔬   💻   🔣   💾   🚲   🧬

Carl Mathias Kobel's Projects

100-days-of-code icon 100-days-of-code

Fork this template for the 100 days journal - to keep yourself accountable (multiple languages available)

aib icon aib

Various core algorithms used in bioinformatics.

bifrost icon bifrost

I made this fork in order to fix some of the issues I stumbled upon during installation. (April 2020)

chimpx icon chimpx

Measuring copy number variation among publicly available Chimpanzee genomes

core-gene-positioner icon core-gene-positioner

🚩👀 This tool shows visualizes the position of the core genes on the contigs of a set of - possibly incomplete - microbial assemblies.

covid19 icon covid19

Bioinformatic pipelines used to assemble SARS-CoV-2 genomes from DK

dram-turnkey icon dram-turnkey

Distilled and Refined Annotation of Metabolism: Turnkey edition with trivial installation. Just provide the data and turn the key.

fragpipe icon fragpipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

gapseq icon gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

gbgc icon gbgc

🦠💪 Investigating gBGC in Rhizobium leguminosarum

gsa icon gsa

Genome Scale Algorithms.

gwf icon gwf

A flexible, pragmatic workflow tool.

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