E. coli outbreak analysis

My posts:

Summaries of genes in E. coli outbreak strain

Prophage:

Plasmids

Typing

SNP analysis

Data releases

Data & availability:

Update June 21. In addition to the 454 scaffold for H112180280, the UK’s Health Protection Agency has now posted Illumina MiSeq data (reads + assembly) for H112180280 and a further 4 isolates: http://www.hpa-bioinformatics.org.uk/lgp/genomes

Update June 17. BGI has now released a ‘complete’ assembly of their isolate, including one chromosome contig, the pAA and IncI plasmids (1 contig each) and a mini plasmid (1 contig).

Update June 16. Note 2 new genomes (454) now available from the Göttingen Genomics Lab, see comments section below for details.

Update June 13. BGI has now formally released their data, including reads, under Creative Commons 0 license. This is the most open license possible, and includes this statement:

The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.

They have set up this page with links to, and details of, all the data available.

A similar formalisation is expected from HPA soon.

June 11.

There are currently three genomes available, TY2482 (BGI) and LB226692 (LifeTech), H112180280 (HPA UK).

Assemblies are available:

Reads of all three are also now available:

Several assemblies annotations are available (see wiki) and the annotated LB226692 genome is now browsable in online tools (Genoscope, PATRIC)

See github wiki for more up-to-date data, annotation & crowdsourced analyses: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki

ScienceScientists Rush to Study Genome of Lethal E. coli [Summary only; subscription required to read full article]

Nature: Phage on the rampage; The German E. coli outbreak: 40 lives and hours of crowdsourced sequence analysis later

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One thought on “E. coli outbreak analysis

  1. Hi Kat,

    we love your blog. Excellent work!
    We just released the 454 data of another two isolates from the German E. coli outbreak. You can find it on our website:
    http://www.g2l.bio.uni-goettingen.de/
    The link to the ftp server is ftp://134.76.70.117/
    User name and password are ‘EAHEC_GOS’.
    Would be great if you could post it on the github E. coli O104:H4 Genome Analysis Crowdsourcing.
    Thanks and keep up the good work!
    Cheers,
    G2L team

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