Portfolio Bioinformatics Tools AnnapotaterA quick SNP annotator for microbial variant analysis. Bio::KmerA Perl module for efficient k-mer counting from biological sequences. Bio::MinimizerPerl module for computing minimizers from biological sequences. CG-PipelineCommand-line pipeline for genome assembly, prediction, and annotation. FastenA toolkit for streaming bioinformatics operations on FASTQ files. File::Find::FastA faster drop-in replacement for Perl's built-in File::Find module. KalamariA curated database of completed genome assemblies with taxonomy IDs for metagenomic classification. LYVE-SETHigh-quality SNP-based phylogenetics for infectious disease outbreak investigations. MLST Hash Template ExampleA worked example of building a genomic epidemiology database using the MLST hash template. MLST-CLICommand-line tools for building and manipulating whole-genome MLST allele databases. MashpitSketch-based genomic surveillance platform for rapid pathogen cluster detection. MashtreeCreate phylogenetic trees using Mash distances for rapid whole-genome analysis. SneakerNetQA/QC pipeline for MiSeq, HiSeq, Ion Torrent, and assembly-only sequencing runs. Suffix::TriePure Perl suffix trie for efficient sequence substring searches. bio-sketch-perlPure Perl implementation of min-hash sketching for genomic sequence comparison. dists2treesA generic pipeline for converting pairwise distance matrices into phylogenetic trees. hash2seqReverse-engineer a sequence from a reference genome and a hash value. pdtkToolkit for interacting with the NCBI Pathogen Detection Portal. Educational Resources Awesome Bioinformatics EducationA curated list of courses, tutorials, and learning resources for bioinformatics. Awesome Bioinformatics JobsA curated list of resources for bioinformatics job seekers. Fundamentals of BioinformaticsCourse materials and exercises covering foundational bioinformatics concepts. Personal Projects MirrorsA site to hold mirrors of certain data. RecipesA collection of recipes I enjoy making. Yearbook TemplateA Jekyll template for generating a yearbook-style website from structured data. Games Doggo ChatA chat-based game featuring dog characters. Elemental MastersA strategy game featuring elemental-based gameplay, built with AI assistance.
