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 use rust/python/nim and other programming languages where suitable. I use git, nextflow, AWS, and machine learning as needed for WGS, WES and other sequencing data. 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 longer projects where I am more integrated than a contractor, but 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 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. If you have a smaller project or something else 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), and nim 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, and QC
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