Resources
A few useful starting points for microbial genomics and reproducible analysis.
Useful for pangenomics, metagenome-resolved analyses, interactive inspection of bins and contigs, and figure-ready visual summaries. I use it when exploratory visualization and genome-centric interpretation need to stay close to the underlying data.
A practical bacterial genomics workflow stack for assembly, annotation, QC, taxonomic characterization, and downstream summaries. Good when processing many isolates with consistent defaults and reproducible outputs matters more than one-off scripting.
Community-maintained Nextflow pipelines that provide solid starting points for RNA-seq, metagenomics, and other common bioinformatics workflows. I treat them as reproducible baselines, then adapt configuration and execution details to local HPC environments when needed.
A strong reference point for making genomic epidemiology and phylogenetic interpretation visually legible. Even outside outbreak-focused work, it is a useful example of how analysis, annotation, and interactive visualization can be combined into something scientists can actually explore.