Pinned Repositories
aribalord
Snakemake pipeline to automate ARIBA analysis and downstream processing
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
Supporting data files for manuscript: 'Australian porcine CC10 E. coli belong to multiple sublineages of a highly diverse global CC10 phylogeny'
custom_DBs
Extra databases for aribalord snakemake pipeline
EZClermont_nextflow_issue
Reproducible example of issue where successful EZClermont runs kill Nextflow workflows
mag
Assembly and binning of metagenomes
snplord
Snakemake pipeline automating SNP phylogeny analysis
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"
ST58_project
Data and scripts for reproducing analysis of the 2021 ST58 manuscript
WGS_produce_ecoli_2019
Data for WGS study of E. coli from produce
CJREID's Repositories
CJREID/CC10_supporting_data
Supporting data files for manuscript: 'Australian porcine CC10 E. coli belong to multiple sublineages of a highly diverse global CC10 phylogeny'
CJREID/snplord
Snakemake pipeline automating SNP phylogeny analysis
CJREID/ST58_project
Data and scripts for reproducing analysis of the 2021 ST58 manuscript
CJREID/aribalord
Snakemake pipeline to automate ARIBA analysis and downstream processing
CJREID/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.
CJREID/custom_DBs
Extra databases for aribalord snakemake pipeline
CJREID/EZClermont_nextflow_issue
Reproducible example of issue where successful EZClermont runs kill Nextflow workflows
CJREID/mag
Assembly and binning of metagenomes
CJREID/MIntO
Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data
CJREID/MVC
Scripts for running secondary analysis on E. coli genomes from the MVC collection
CJREID/phylosiftlord
snakemake phylosift
CJREID/plasmidlord
sdkla;sdhfajklsdffs
CJREID/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"
CJREID/WGS_produce_ecoli_2019
Data for WGS study of E. coli from produce
CJREID/pb-metagenomics-tools
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
CJREID/plasmidmapR
A package for the mass calculation and visualisation of reference plasmid coverage within whole genome sequence datasets
CJREID/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
CJREID/Roary
Rapid large-scale prokaryote pan genome analysis
CJREID/snplord-nf
Nextflow pipeline for bacterial SNP-based phylogenetic analysis
CJREID/ST127
Scripts to run analysis associated with 2021 ST127 manuscript
CJREID/ST372
Scripts for analysis of E. coli ST372 genomes