Shane Mccarthy
Head Of Genome Assembly at Wellcome Sanger Institute
Cambridge, England, United Kingdom
Summary
🤩
Rockstar🎓
Top SchoolShane Mccarthy is a seasoned genomics software leader with 15 years of experience bridging computational biology and production bioinformatics, currently heading Genome Assembly at the Wellcome Sanger Institute. He brings deep C and backend expertise from sustained contributions to high-profile open-source projects like htslib, bcftools and samtools, improving core VCF/BCF handling, tooling and test infrastructure used across the sequencing community. His background mixes rigorous academic training (PhD in Physics, MPhil in Computational Biology) with leadership of large-scale resequencing teams, giving him a rare blend of hands-on algorithmic skill and program-level delivery. Known for pragmatic engineering—adding robust error handling, new commands and practical utilities like vcfsubset—he focuses on shipping reliable, production-ready software that scales with genomics projects.
15 years of coding experience
14 years of employment as a software developer
PhD, Physics, PhD, Physics at The University of Western AustraliaMPhil, Computational Biology, MPhil, Computational Biology at University of Cambridge
Github Skills (19)
algorithm10
algorithms10
biom10
testing10
c-programming10
c1110
data-structure10
vcf-files10
c1710
htslib10
bioinformatics10
data-structures10
command-line-tool10
fileio9
file-access9
Programming languages (12)
Github contributions (5)
samtools/samtools
Oct 2013 - May 2020
Tools (written in C using htslib) for manipulating next-generation sequencing data
Role in this project:
Back-end Developer & QA Engineer / Test Automation Engineer
Back-end Developer & QA Engineer / Test Automation EngineerContributions:19 commits, 10 PRs, 5 branches in 6 years 8 months
Contributions summary:Shane primarily contributed to improving the robustness and functionality of the `samtools` command-line tools. They implemented error handling, specifically for cases where input files, such as BED files, could not be read. Additionally, they added new features, such as the `dict` command for creating sequence dictionary files, and incorporated tests for the `samtools index` command, enhancing the testing infrastructure. Their work also involved deprecating older options and updating documentation for clarity.
next-generationsequencing-datanext-generation-sequencinggenomicssequencing
samtools/bcftools
Oct 2013 - Sep 2017
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
Role in this project:Back-end Developer
Back-end DeveloperContributions:231 commits, 102 PRs, 212 pushes in 3 years 11 months
Contributions summary:Shane primarily contributed to the core functionality of the BCFtools library, making key modifications to existing code and fixing minor bugs. Their work involved initializing mappings, updating APIs for genotype analysis, addressing private option issues within VCF subsetting, and performing various cleanup tasks to improve code quality. The user interacted with key components of the library, including mcall.c, vcfstats.c, vcfsubset.c, and test files to ensure functionality and maintainability.
bcftoolsinstructionsinstallationsamtools
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