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jonas-fuchs/README.md

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Welcome 🦊

I am currently working as a Post-Doc at the Institute for Virology in Freiburg leading the in-house NGS sequencing laboratory. 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

Top Langs

Software 💾

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

  • BAMdash Aggregate your virus sequencing results into an interactive plot.
  • varVAMP Design primers for PCR on highly variable alignments.
  • virHEAT Compare vcf files as a heatmap.

stats

Publications 📜

Pinned

  1. varVAMP varVAMP Public

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

    Python 20 8

  2. BAMdash BAMdash Public

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

    Python 20 1

  3. virHEAT virHEAT Public

    Visualize microbial evolution at the SNP level!

    Python 10 4

  4. 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…

    1

  5. SARS-CoV-2-analyses SARS-CoV-2-analyses Public

    Collection of R scripts for SARS-CoV-2 (variant) analyses

    R 12 1