About
I am a genomics researcher and software developer focused on creating useful, simple, fast and reliable tools for variant analysis and genomic data processing. I am looking for contract work that is interesting and impactful and where my skills can be best utilized.
Work With Me¶
I am interested in substantial projects, but with less commitment (to you) than a staff member. A model I have in mind is 16 weeks (~⅓rd year) of focused work for $25K commitment. This could be an alternative to committing to a staff bioinformatician. It could be for a pilot study or a focused project or certainly a long-term collaboration. Most universities can support this via vendor contract or even simpler. This is an idea, if you have another mode of work or a project in mind, feel free to contact me.
Recommendations¶
Key Projects¶
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mosdepth
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. Written in Nim for maximum performance.
Mosdepth: quick coverage calculation for genomes and exomes. -
somalier
Fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs. Essential for quality control in genomic studies.
Somalier: rapid relatedness estimation for cancer and germline studies using efficient sketches. -
slivar
Genetic variant expressions, annotation, and filtering for great good. Streamlines variant analysis workflows.
Effective variant filtering and expected candidate variant yield in studies of rare human disease. -
vcfanno
Annotate a VCF with other VCFs/BEDs/tabixed files. Written in Go for speed and reliability.
VCFanno: fast, flexible annotation of genetic variants. -
cyvcf2
Cython + htslib for fast VCF and BCF processing. Core library for many Python-based genomic tools.
cyvcf2: fast, flexible variant analysis with Python/Cython. -
echtvar
Using all the bits for echt rapid variant annotation and filtering. Written in Rust for maximum performance.
Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels.
Technical Expertise¶
I have extensive experience in developing in rust, python/cython (extension modules and entire software), nim and go for high-performance bioinformatics tools. My expertise includes genomics, variant analysis, and performance optimization for large-scale genomic data processing.
My work has been in developing efficient algorithms, largely in variant filtering, annotation, and QC. I like to add scripting capabilities to command-line tools to give maximum flexibility.
Recent Activity¶
Check out the blog section for the latest posts and updates on my research and software development work.
Connect¶
- GitHub: github.com/brentp
- Google Scholar: Profile
- Location: Oregon, USA
- Twitter: @brent_p