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ariba

Antimicrobial Resistance Identification By Assembly

assemblerflow

A NextFlow pipeline assembler for bacterial genomics

bioconda-recipes

Conda recipes for the bioconda channel.

bioinfclinic

Introduction to datawrangling with Pandas and trees with ggtree - for MDU

cgmlst-dists

🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables

chewbbaca_singularity

clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

coreugate

A simple cgMLST pipeline

coreuscan

A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA

dash-phylogeny

Interactive phylogeny trees with Dash

datasets

Benchmark datasets for WGS analysis

gram

Vector graphics in Python. Phylogenetic tree diagrams. http://gram.nhm.ac.uk/

hehackshehack

health hack repository 2015

lissero

In silico serotype prediction for Listeria monocytogenes

maskrc-svg

Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG

multi_assembler_singularity

nextflow-shovill

🔗 A simple nextflow of shovill for running multiple samples at once on multiple cores computer or HPC (i.e. slurm, sge,...)

pan-zoom

Pan and zoom events for everybody

phaster_scripts

Small utility script to submit genomes to PHASTER for phage detection

phylocanvas

phylocanvas-plugin-ajax

Load tree format strings via Ajax.

phylocanvas-plugin-context-menu

Contextual functions for Phylocanvas

phylocanvas-plugin-history

Visual history for Phylocanvas

phylocanvas-plugin-metadata

Display binary data adjacent to tree leaves.

phylocanvas-plugin-scalebar

Visual scale-bar for Phylocanvas

phylocanvas-quickstart

Phylocanvas with core plugins preloaded for convenience.

playground

Trying out ideas

pysingscore

Python3 Implementation of SingScore

sakai-vue

seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads