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


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)
DatabaseInstructions | 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 (include database of Klebsiella capsule and O antigen types)
Author/contact: Kelly Wyres & Ryan Wick
Code – https://github.com/katholt/kaptive
Paper – Wyres et al, Microbial Genomics 2016
Kaptive Web  – http://kaptive.holtlab.net (online version: upload your own genomes)
Kaptive Web & O typing – Wick et al, J Clin Micro 2018


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, MGen 2018


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


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

 


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

 

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