I support research groups by performing bioinformatic analyses and developing workflows on request. My bioinformatic expertise focuses on de novo genome assembly, but I am also able to perform other sequence based analyses, such as variant calling, amplicon analysis, ancient DNA analysis, and more. In addition to my support work, I'm currently helping develop a genome assembly and annotation workflow for the Swedish Pilot Project in the Earth Biogenome Project. As part of my support work, I aim to make my work reproducible, using version control, workflow managers, and containerized software. I use this template as the starting point for my work, keeping data, files, and code organised, and hopefully easy to follow and extend for those I support.
I'm adept at programming, and writing workflows in particular. I'm well versed in Bash scripting, as well being able to use Perl, awk, sed, and R too. I write workflows using the Nextflow workflow language, based on Groovy. I have used various other languages in the past including Java, C, C++, Turing, Haskell, Prolog, and Assembly, including database languages such as PostgresQL. I'm familiar with various markup and serialization languages such as Markdown, HTML, Wiki Markup, Latex, and YAML. In my work, I regularity use Git, Docker, and Singularity, as well as Github Actions and Makefiles for automation, and Gitpod as a development environment.
I contribute to the nf-core and Nextflow community, helping answer questions and develop best-practice workflows.
Expand for my notable contributions
- Driving nf-core to use native syntax for workflow data publishing and tool parameter passing
- Hear Dr H Patel explain the work at the nf-core Hackathon on Youtube.
- Adding a Gitpod dev environment for testing workflows, tools, and modules
- Enabling the process
when:declaration to be used from a configuration file.- Template update.
- Update existing modules.
- Documentation update.
- Module Linter update.
- Hear Dr M Garcia explain how he used this to tidy up the nf-core Sarek codebase on YouTube
- Code reviews for large pipelines such as nf-core/Sarek, nf-core/HiCar and nf-core/Metatdenovo.
- The addition of several tools for genome assembly to nf-core/modules
I am a certified Carpentries Instructor. I have helped develop The Carpentries Introduction to Nextflow.
As a bioinformatician, I use a variety of tools to aid my work. These are tools I have used in recent years.
mindmap
root((Tools))
Programming Languages
Bash
Awk
Nextflow/Groovy
R
Perl
SQL
Jq
Python
Package management
Conda/Mamba
Docker
Singularity/Apptainer
Virtual env
Modules
Version control
Git
Github
Markup
Markdown
Latex
Wikitext
HTML
Diagramming
Mermaid
Literate programming
Quarto
RMarkdown
Project management
Github
Trello
Confluence
Notion
Automation
Github actions
Make
Nextflow
Quarto
Developer environments
MacOs
Linux
Gitpod
HPC