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bactopia

A flexible pipeline for complete analysis of bacterial genomes

bio-courses

Tutorials for bacterial WGS

bio-tradis

A set of tools to analyse the output from TraDIS analyses

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

clinker

Gene cluster comparison figure generator

dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

ggtreeextra

:lemon: Add Geom Layers On Circular Or Other Layout Tree Of “ggtree”

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

maskrc-svg

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

mlst

:id: Scan contig files against PubMLST typing schemes

ncbimeta

Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).

nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

pirate

A toolbox for pangenome analysis and threshold evaluation.

plottree

r-graph-gallery

A website that displays hundreds of R charts with their code

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

snpbac

SNP and variant calling pipeline for bacteria

treedata-book

:books: a complete reference book for treeio, tidytree and ggtree packages

treewas