cjreid Goto Github PK
Name: Cameron Reid
Type: User
Company: CSIRO
Twitter: camreid90
Location: Adelaide
Name: Cameron Reid
Type: User
Company: CSIRO
Twitter: camreid90
Location: Adelaide
Snakemake pipeline to automate ARIBA analysis and downstream processing
Data analysis and visualisation for manuscript "F plasmids in Escherichia coli bloodstream infections" by Reid C.J., Cummins M.L. and Djordjevic S.P.
Supporting data files for manuscript: 'Australian porcine CC10 E. coli belong to multiple sublineages of a highly diverse global CC10 phylogeny'
Extra databases for aribalord snakemake pipeline
Reproducible example of issue where successful EZClermont runs kill Nextflow workflows
Assembly and binning of metagenomes
Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data
Scripts for running secondary analysis on E. coli genomes from the MVC collection
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
snakemake phylosift
sdkla;sdhfajklsdffs
A package for the mass calculation and visualisation of reference plasmid coverage within whole genome sequence datasets
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Rapid large-scale prokaryote pan genome analysis
Snakemake pipeline automating SNP phylogeny analysis
Nextflow pipeline for bacterial SNP-based phylogenetic analysis
Scripts to run analysis associated with 2021 ST127 manuscript
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"
Scripts for analysis of E. coli ST372 genomes
Data and scripts for reproducing analysis of the 2021 ST58 manuscript
Data for WGS study of E. coli from produce
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