Yossi Farjoun
Principal Computational Biologist
Montreal, Quebec, Canada
Summary
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Rockstar🎓
Top SchoolYossi Farjoun is a Principal Computational Biologist with 13 years of experience blending applied mathematics, numerical simulation and software engineering to solve genomics data challenges. Based in Montreal, he has driven production-grade tooling and test-driven improvements at the Broad Institute and contributed bug fixes and rigorous tests to flagship open-source projects like GATK, Picard and htsjdk. His work focuses on robust data processing—fixing edge-case read clipping, index overflows and VCF writer bugs—bringing both deep domain knowledge and meticulous backend engineering to sequencing pipelines. Trained as a PhD in Applied Mathematics (UC Berkeley), he pairs theoretical modeling experience with practical software craftsmanship, and has a history of teaching and researcher roles that inform his clear, well-tested solutions.
13 years of coding experience
12 years of employment as a software developer
PhD Applied Mathematics, PhD Applied Mathematics at University of California, BerkeleyGivan GonenWest Lafayette High SchoolBSc Mathematics Physics, BSc Mathematics Physics at The Hebrew University of JerusalemHigh School Diploma, High School Diploma at Leyada
English, Hebrew, Spanish
Stackoverflow
2,218reputation
856kreached
7answers
10questions
command-line
top-5%
truncate
top-5%
scripting
top-5%
bash
top-5%
Github Skills (25)
bam10
testing10
java10
vcf-files10
sam10
javas10
bioinformatics10
genomics10
scripting9
debug9
debugging9
truncate9
bash9
command-line9
java-api8
Programming languages (18)
Github contributions (5)
broadinstitute/picard
May 2013 - Jan 2023
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:118 reviews, 440 commits, 453 PRs in 9 years 9 months
Contributions summary:Yossi contributed to the testing and debugging of the `picard` repository, which is a suite of command-line tools for manipulating high-throughput sequencing data. Contributions included adding tests for the `SeekableBufferedStream` and correcting an issue in the `insertSizeHistogram.R` script. Furthermore, the user worked on fixing issues in the VCF writer by closing files and ensuring the accurate handling of indels. The user also added and maintained various unit tests.
sequencebamcramcommand-line-toolsfasta
samtools/htsjdk
Jul 2014 - Jul 2021
A Java API for high-throughput sequencing data (HTS) formats.
Role in this project:Back-end Developer & Test Automation Engineer
Back-end Developer & Test Automation EngineerContributions:13 reviews, 185 commits, 229 PRs in 7 years 2 months
Contributions summary:Yossi primarily contributed to improving the codebase through bug fixes and adding tests. They worked on refactoring existing code, specifically addressing an overflow bug in index writing and implementing checks in interval lists. The user also made contributions to various test files, adding a wide range of tests including tests for the VCFFileReader and the SAMRecord, demonstrating proficiency in test-driven development.
sequencednabamcramsequencing-data
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