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bi ba booop i am a robot
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bi ba booop i am a robot
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Achievement: Pair Extraordinairex2Achievement: StarstruckAchievement: Pull Sharkx2Achievement: YOLO

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jonas-fuchs/README.md

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Welcome 🦊

I am a Junior Group Leader at the Institute for Virology in Freiburg. We focus on viral genomics and intra-host evolution of diverse pathogens (Hepatitis E virus, SARS-CoV-2, Influenza A, MPXV and HSV-1). I started bioinformatics at the beginning of the SARS-CoV-2 pandemic and have been in love with big data, genomics, metagenomics, coding and pyhlogenetics ever since. I am a super weird mixture of wet-lab molecular virologist, bioinformatician, data scientist, NGS specialist, epidemiologist, clinical scientist and nerd.

Skills ✔️

My Skillssnakemake

Software 💾

I am working on software for viral genomics. Available through pip and conda.

  • ResPro Antiviral resistance profiling for any virus.
  • MSAexplorer Multiple Sequence Alignment graphing library on top of matplotlib.
  • varVAMP Design primers for PCR on highly variable alignments.
  • BAMdash Aggregate your virus sequencing results into an interactive plot.
  • virHEAT Compare vcf files as a heatmap.

Some selected publications 📜

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  1. the-foxlab/ResistanceProfiler the-foxlab/ResistanceProfiler Public

    Antiviral resistance analysis framework for any virus

    Python 3

  2. varVAMP varVAMP Public

    Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

    Python 55 12

  3. MSAexplorer MSAexplorer Public

    A python graphing library for plotting multiple sequence alignments. An app build on top that runs everything in your browser.

    Python 28 2

  4. BAMdash BAMdash Public

    create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

    Python 58 4

  5. virHEAT virHEAT Public

    Visualize microbial evolution at the SNP level!

    Python 16 5

  6. ViralPrimerSchemes ViralPrimerSchemes Public

    Repository for pan-spefic primers designed for tiled full genome sequencing or qPCR of viral pathogens. Pathogens include amongst others Hepatitis E virus, Hepatitis A virus, Poliovirus and SARS-CO…

    7