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Cameron Reid's Projects

aribalord icon aribalord

Snakemake pipeline to automate ARIBA analysis and downstream processing

bsi-f-plasmids icon bsi-f-plasmids

Data analysis and visualisation for manuscript "F plasmids in Escherichia coli bloodstream infections" by Reid C.J., Cummins M.L. and Djordjevic S.P.

cc10_supporting_data icon cc10_supporting_data

Supporting data files for manuscript: 'Australian porcine CC10 E. coli belong to multiple sublineages of a highly diverse global CC10 phylogeny'

custom_dbs icon custom_dbs

Extra databases for aribalord snakemake pipeline

mag icon mag

Assembly and binning of metagenomes

minto icon minto

Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data

mvc icon mvc

Scripts for running secondary analysis on E. coli genomes from the MVC collection

plasmidmapr icon plasmidmapr

A package for the mass calculation and visualisation of reference plasmid coverage within whole genome sequence datasets

rnaseq icon rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

roary icon roary

Rapid large-scale prokaryote pan genome analysis

snplord icon snplord

Snakemake pipeline automating SNP phylogeny analysis

snplord-nf icon snplord-nf

Nextflow pipeline for bacterial SNP-based phylogenetic analysis

st127 icon st127

Scripts to run analysis associated with 2021 ST127 manuscript

st131-h22_supporting_data icon st131-h22_supporting_data

Supporting data for draft manuscript "Clonal ST131-H22 E. coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids"

st372 icon st372

Scripts for analysis of E. coli ST372 genomes

st58_project icon st58_project

Data and scripts for reproducing analysis of the 2021 ST58 manuscript

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