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 collaborative contract work that is interesting and impactful and where my skills can be best utilized.
Work With Me¶
- Are you struggling with quality control problems in your genomic studies?
- Is your variant processingn pipeline for clinical pipelines slow or incomplete?
- Do you need help with custom visualizations, a well-defined genomics tools or analyses?
I am interested in substantial projects, but with less commitment (to you) than a staff member. My preferred model is 16 weeks (~⅓rd year) of focused work of at least 1 day per week for a $25K commitment. I intend to have 2-3 projects at any given time.
This model is an alternative to committing to a staff bioinformatician. I am also open to projects that match my expertise and interest, if you have questions or a project, please contact me.
Recommendations¶
Key Projects¶
Here are some of my projects, each with an open-source repository that I still maintain and a publication describing it's use.
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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