Software

bandage_logoBandage – Assembly Graph Visualisation
Author/contact: Ryan Wick
Code – http://rrwick.github.io/Bandage/
Paper – Wick et al, Bioinformatics 2015
Blog posts and examples

unicycler_logoUnicycler – Hybrid assembly of bacterial genomes using short and long reads
Author/contact: Ryan Wick
Code – https://github.com/rrwick/Unicycler
Paper – Wick et al, PLoS Comp Biol 2017

Trycycler – Consensus based assemblies for bacterial genomes using long reads
Author/contact: Ryan Wick
Code – https://github.com/rrwick/Trycycler

Paper – Wick et al, Genome Biology 2021

Polypolish – Polypolish: short-read polishing of long-read bacterial genome assemblieslogo_transparent

Author/contact: Ryan Wick
Code – https://github.com/rrwick/Polypolish
Paper – Wick et al, PLoS Comp Biol 2022

Deepbinner – Demultiplexing of raw (non-base called) nanopore reads

Author/contact: Ryan Wick
Code – https://github.com/rrwick/Deepbinner
Paper – Wick et al, PLoS Comp Biol 2018

ISMapper – Identifying insertion sequences in bacterial genomes from short read sequence data
Author/contact: Jane Hawkey
Code – https://github.com/jhawkey/IS_mapper
Paper – Hawkey et al, BMC Genomics 2015
Blog posts and examples

SRST2 – Short Read Sequence Typing for Bacterial Pathogens (MLST, resistance gene typing, etc)
Author/contact: Kat Holt
Code – https://github.com/katholt/srst2
Paper – Inouye et al, Genome Medicine 2014
Blog post – Behind the paper

Specialist databases for E. coli typing with SRST2:
• EcOH (E. coli serotype prediction)
Database | Instructions | Ingle et al, Microbial Genomics 2016
• LEE pathogenicity island (E. coli type 3 secretion system)
Database | Instructions | Ingle et al, Nature Microbiology 2016
Author/contact: Danielle Ingle & Kat Holt

kaptive_logoKaptive – Typing capsule & O antigen biosynthesis loci from genome assemblies (includes database of Klebsiella capsule and O antigen types, and A. baumannii K and OC loci)
Author/contact: Kelly Wyres & Ryan Wick
Code – https://github.com/katholt/kaptive
Paper – Wyres et al, Microbial Genomics 2016
Kaptive Web  – https://kaptive-web.erc.monash.edu (online version: upload your own genomes)
Kaptive Web & O typing – Wick et al, J Clin Micro 2018

Kaptive v2, with new K loci and O2 subtyping – Lam et al, Microbial Genomics 2022

Acinetobacter baumannii K and OCL typing – Wyres et al, Microbial Genomics 2020 (via collaboration with Jo Kenyon at QUT)

Kleborate – Genotyping Klebsiella from genome assemblieskleborate_logo
(including MLST, virulence loci & resistance genes)
Author/contact: Kat Holt, Margaret Lam & Ryan Wick
Code – https://github.com/katholt/Kleborate
Paper – Lam et al, Nature Communications 2021

Kleborate Viz (R Shiny app to visualise results) – https://kleborate.erc.monash.edu/

Fig1_noH58_clade_colours_subcladebg_190515_labelled_EDGenoTyphi – Genotyping scheme for Salmonella Typhi (typhoid)
Author/contact: Kat Holt & Zoe Dyson
Code – https://github.com/katholt/genotyphi
Paper – Wong et al, Nature Communications 2016
Blog post – Global Genomic Framework for Typhoid

Update paper – Dyson & Holt, Journal of Infectious Diseases 2021

Shigella sonnei Typing – Genotyping scheme for Shigella sonnei (dysentery)
Author/contact: Kat Holt & Jane Hawkey
Code – https://github.com/katholt/sonneityping
Paper – Hawkey et al, Nature Communications 2021

hicap – Capsule locus detection and serotype prediction for Haemophilus influenzae
Author/contact: Kat Holt & Stephen Watts
Code – https://github.com/scwatts/hicap
Paper – Watts & Holt, Journal of Clinical Microbiology 2019

RedDog – Mapping-based phylogenomics pipelinereddog_logo
Author: David Edwards
Code & tutorial – https://github.com/katholt/RedDog

Nextflow version – https://github.com/katholt/reddog-nf

FastSpar – Rapid and scalable correlation estimation for compositional data
A C++ implementation of the SparCC algorithm, with more accurate p-value calculation, and fast implementation of dbOTU3 algorithm
Author/contact: Stephen Watts
Code – https://github.com/scwatts/FastSpar
Paper – Watts et al, Bioinformatics 2018

BadRead – Long read simulator
Designed to facilitate testing of tools for long-read analysis, imitates  problems commonly encountered in real long-read sets (chimeras, low-quality regions, systematic basecalling errors etc)
Author/contact: Ryan Wick
Code – https://github.com/rrwick/Badread
Paper – Wick RR, Journal of Open Source Software 2019

SNPPar – Efficient identification and annotation of homoplasies and convergent evolution from bacterial whole-genome data
Author: David Edwards
Code – https://github.com/d-j-e/SNPPar
Paper – Edwards et al, Microbial Genomics 2021