Florian Breitwieser
Principal Software Engineer at SOPHiA GENETICS
Lausanne, Vaud, Switzerland
Summary
🤩
Rockstar🎓
Top SchoolFlorian Breitwieser is a Principal Software Engineer based in Lausanne with 12 years of experience building robust bioinformatics and data-processing systems. Currently leading technical efforts at SOPHiA GENETICS, he combines hands-on backend development with team leadership, progressing from senior engineer to associate manager and technical lead before his current role. His open-source contributions include impactful backend work on widely used genomics tools such as MMseqs2 and samtools—improving taxonomy reporting and sequencing coverage analysis—demonstrating deep domain expertise in NGS tooling. With a strong academic foundation including a PhD and postdoc in bioinformatics and computational proteomics, he bridges research and production by turning complex statistical methods into reliable software. Colleagues rely on him for thoughtful refactors, pragmatic feature additions, and enhancements that improve usability (for example, better progress indicators and reporting options) beyond core algorithms.
12 years of coding experience
10 years of employment as a software developer
Doctor of Philosophy (PhD) Medical Statistics Biostatistics and Complex Systems, Doctor of Philosophy (PhD) Medical Statistics Biostatistics and Complex Systems at Medical University of Vienna, AustriaJohns Hopkins UniversityDiplom-Ingenieur (FH) Bioinformatics, Diplom-Ingenieur (FH) Bioinformatics at Hagenberg Campus - FH Upper AustriaMaster of Science (MS) Bioinformatics, Master of Science (MS) Bioinformatics at Upper Austrian University of Applied Sciences
German, English, Spanish, French
Github Skills (17)
text-alignment10
c-language10
taxonomy10
command-line-interface10
c1110
c1710
htslib10
command-line10
text-align10
bioinformatics10
cprogramming-language10
data-analysis10
develop9
algorithm9
algorithms9
Programming languages (13)
Github contributions (5)
samtools/samtools
Nov 2018 - May 2019
Tools (written in C using htslib) for manipulating next-generation sequencing data
Role in this project:
Back-end Developer
Back-end DeveloperContributions:11 commits, 1 PR, 29 comments in 6 months
Contributions summary:Florian primarily focused on improving the `samtools coverage` command. Their contributions included adding the command and implementing its core functionality to calculate and display coverage statistics. Further commits involved refactoring the code, enhancing the display of histograms, and adding functionality for filtering and formatting the output. The user also fixed bugs and incorporated feedback to improve the command's overall usability and presentation.
next-generationsequencing-datanext-generation-sequencinggenomicssequencing
soedinglab/MMseqs2
Apr 2019 - Jun 2019
MMseqs2: ultra fast and sensitive search and clustering suite
Role in this project:Back-end Developer
Back-end DeveloperContributions:10 commits, 3 PRs, 6 comments in 1 month
Contributions summary:Florian primarily contributed to the core backend functionality of the MMseqs2 project. Their work focused on enhancing the NcbiTaxonomy module, including refactoring the code, adding features such as a Kraken-style taxonomy report, and implementing options like `--taxLineage`. These changes indicate an effort to improve the taxonomy analysis capabilities of the software. The user also improved the progress bar for the project.
profile-searchmetagenomicsalignmentultrammseqs
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