Reference laboratories

European Union Reference Laboratory for Escherichia coli

E. coli genomics

This section is meant to provide the user information related with the E. coli genomics and Next Generation Sequencing (NGS) applied to the study of pathogenic E. coli. Efforts will be done to maintain the section constantly updated with the latest releases in the sector.  

Information on the updates available will be pushed to all the EU NRLs through the “Focus on” mailing list. If you wish to be included in the recipients’ list, send an E-mail to crl.vtec@iss.it.  

This section may also feature downloadable material, including documents related with the EURL for E. coli initiatives in the field, as well as links to usable tools to perform local analyses of NGS data.  

All the software and tools included in the list are freeware and are made available directly from the authors’ websites.  

Additional links are provided, which direct the user to the web environments where it is possible to remotely run analyses using NGS data.  

This section is also the portal to access the EURL VTEC-managed Galaxy platform ARIES. It contains tools and workflows developed by the EURL for E. coli and specifically intended for analysing E. coli genomes, as well as other bioinformatics, available on the Galaxy tool-shed, for a standard QC and analysis of NGS data.  

Please note that more details on workflows and tools useful for producing, evaluating and analysing NGS data are available in the webpage dedicated to the activities of the Inter-EURLs working group on NGS (see below). 

 

Related links 

Center for Genomic Epidemiology (Technical University of Denmark)  

Multi Locus Sequence Typing of E. coli at the University of Warwick (Sanger sequencing)  

EnteroBase Online resource for analyzing and visualizing genomic variation of Escherichia/Shigella strains 

E. coli reference genomes at NCBI  

PROKKA by Victorian Bioinformatics Consortium for genome annotation  

RAST Rapid Annotation using Subsystem Technology  

MAUVE Multiple Genome Alignment  

BLAST Ring Image Generator (BRIG) for the display of circular comparisons between a large number of genomes, with a focus on handling genome assembly data 

Tablet: A high-performance graphical viewer for NGS assemblies and alignments  

Integrative Genomics Viewer (IGV): a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. 

FigTree: a graphical viewer of phylogenetic trees 

PHYLOViZ Online: Web-based tool for visualization, phylogenetic inference, analysis and sharing