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E. coli genomics

E. coli Genomics: Next Generation Sequencing (NGS) applied to the study of pathogenic E. coli

This section is meant to give the user access to information related with the E. coli genomics, with emphasis on 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 NRL through the “Focus on” mailing list and to any other user via the RSS channel, upon subscription.
This section also features downloadable material, including documents related with the EU-RL for E. coli initiatives in the field, as well as usable tools to perform local analyses of NGS data.
All the softwares and tools included in the list are freeware and are made available directly from the authors’ websites.
Additional links are provided that 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 Galaxy platform ARIES installed on the ISS servers.
It contains tools and workflow developed by the EU-RL 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 (under construction).


The Galaxy platform ARIES is accessible through this link: https://www.iss.it/site/aries


Related links:

Center for Genomic Epidemiology (Technical University of Denmark)
Multi Locus Sequence Typing of E. coli at the University of Warwick (Sanger sequencing)
E. coli reference genomes at NCBI
VelvetOptimizer de novo assembler by Victorian Bioinformatics Consortium for genome annotation
Sequence assembly with MIRA 4
PROKKA by Victorian Bioinformatics Consortium for genome annotation
RAST Rapid Annotation using Subsystem Technology
MAUVE Multiple Genome Alignment
BLAST Ring Image Generator (BRIG)
Galaxy CRS4 Orione (data intensive biology)
Tablet: A high-performance graphical viewer for NGS assemblies and alignments
Integrated Genome Browser (IGB). A piece of software to browse genomic data.

Published 15-04-2015 in E. coli genomics , last update 15-06-2016

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