Nils Homer
Founding Partner at Fulcrum Genomics LLC
Greater Phoenix Area United States
Summary
🤩
Rockstar🎓
Top SchoolNils Homer is a founding partner and bioinformatics software leader with over 16 years of hands-on experience building algorithms and production software for genomic data analysis. He founded Fulcrum Genomics and co-developed fgbio, an open-source toolkit widely adopted by the community, and has driven core contributions to flagship projects such as GATK, samtools/htsjdk, bwa, and Snakemake. His work spans low-level C/Java/Python development, CI/CD and package maintenance (notably maintaining recipes in bioconda), and production engineering for high-throughput pipelines and clinical genomics. Nils has advised hardware-accelerated sequencing analytics (DRAGEN) and led engineering teams at the Broad Institute, blending research-grade algorithm design with scalable, production-ready systems. He pairs a PhD-level algorithmic background with pragmatic DevOps and back-end skills, frequently fixing tricky interoperability and format issues across the genomics toolchain. Based in Greater Phoenix, he combines entrepreneurial drive with deep open-source stewardship that quietly underpins many sequencing workflows.
16 years of coding experience
9 years of employment as a software developer
PHD, Computer Science, PHD, Computer Science at University of California, Los AngelesBA, Mathematics and Computer Science, BA, Mathematics and Computer Science at Colgate University
Swedish, English
Stackoverflow
1reputation
140reached
1answer
1question
Github Skills (63)
algorithm10
data-visualizations10
algorithms10
static-typing10
snakemake10
variants10
python10
package-management10
bam10
scripting10
dynamic-typing10
ram10
analyse10
data-visualisation10
conda10
Programming languages (25)
Github contributions (5)
samtools/htsjdk
Jun 2014 - Feb 2021
A Java API for high-throughput sequencing data (HTS) formats.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:18 reviews, 108 commits, 86 PRs in 6 years 8 months
Contributions summary:Nils made several significant contributions to the `htsjdk` Java API, primarily focused on enhancing and maintaining the VCF (Variant Call Format) handling capabilities. Their work included updating the VCF header to version 4.2, modifying and improving the `DuplicateSet` class, and adding utility methods to clip overlapping bases. Furthermore, the user implemented bug fixes within the codebase, including a compile warning in `ProgressLogger` and issues with the `SamLocusAndReferenceIterator` and SAM flag field.
sequencednabamcramsequencing-data
broadinstitute/picard
Jun 2014 - Feb 2021
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 & Bioinformatics Engineer
Back-end Developer & Bioinformatics EngineerContributions:8 reviews, 164 commits, 173 PRs in 6 years 9 months
Contributions summary:Nils contributed to the development of the Picard suite, a set of command-line tools for manipulating high-throughput sequencing data. Their work involved implementing new tools, such as `CollectBaseDistributionByCycle`, and modifying existing ones, specifically in the area of base quality and mean quality analysis. Additionally, the user demonstrated skills in bug fixing within the `BedToIntervalList` tool and significant refactoring of core components to support a single JAR approach for easier tool access.
sequencebamcramcommand-line-toolsfasta
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