Mark Renton's starred repositories
PhyloTrace
PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.
public_health_bioinformatics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
SyntenyFinder
SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.
AllTheBacteria
Follow up to Grace Blackwell's 661k dataset, for 2023
ecoli_serotyping
In silico prediction of E. coli serotype
awk-hack-the-planet
Source code repo for Ben Porter (FreedomBen)'s free course on Awk (originally a talk at Linux Fest Northwest 2019 and 2020)
assembly_accuracy
tools for assessing the accuracy of genome assemblies
dragonflye
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
genomics_adventure
Workshop on Genomics - Genomics Adventure
awesome-nanopore
A curated list of awesome nanopore analysis tools.
ExpansionHunterDenovo
A suite of tools for detecting expansions of short tandem repeats