Nils Homer
Summary
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RockstarNils Homer is a founding partner of Fulcrum Genomics and a genomics software leader with 16 years of experience building algorithms and production systems that span research and clinical sequencing. He co-authored the SAM specification and has helped steer tools and papers that collectively exceed 82,000 citations, while his fgbio toolkit has been downloaded over 300,000 times and is widely used for molecular-barcoded, ultra-accurate variant detection. He advised Edico Genome on algorithms that evolved into Illumina’s DRAGEN platform and is an active contributor to core projects like BWA, htsjdk/samtools, GATK and Picard. At the Broad Institute he led teams delivering pipeline and platform software that powers the institute’s large-scale sequencing operations. With a PhD in Computer Science from UCLA, he combines deep algorithmic expertise with hands-on engineering, DevOps and productization across academia, startups and clinical diagnostics.
16 years of coding experience
Stackoverflow
1reputation
140reached
1answer
1question
Github Skills (69)
snakemake10
variants10
python10
package-management10
analyse10
c1110
c1710
javas10
gatk10
picard10
command-line-tool10
genomics10
reporting-services10
bam10
ram10
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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