June 13. BGI has now formally released their data, including Illumina reads, under Creative Commons 0 (CC0) 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 … Continue reading
In the German outbreak bacteria, as in most E. coli, plenty of horizontal transfer has gone on to create the genome we are now looking at. I’ve done about all I’m going to on this analysis, at least until some more complete data is released… but I did generate a summary plot and have a … Continue reading
A brief look at the genes present in the outbreak strains and not in the reference strain Ec55989 reveals a large number of contigs with similarity to the plasmid pEC_Bactec (by NCBI blast)… a quick MUMmer alignment and ACT visualisation confirms that an IncI plasmid similar to pEC_bactec (GU371927.1, ref here) is present, including the … Continue reading
So two sequences have so far been released relating to the EHEC outbreak in Europe, see details here and links to public data & analyses here on Nick Loman’s blog: http://pathogenomics.bham.ac.uk/blog/2011/06/ehec-genome-assembly/ For the first sequence, Ty2482, BGI has release fastqs and an assembly (methods undescribed); Nick Loman did an assembly using MIRA. The second sequence … Continue reading
This is a shameless plug for an article and accompanying tutorial I’ve just published together with David Edwards, my excellent MSc Bioinformatics student from the University of Melbourne. It’s currently available as a PDF pre-pub from BMC Microbial Informatics and Experimentation, but the web version will be available soon. The accompanying tutorial is available here. The idea for … Continue reading
Two new genomes were released today (well today my time, yesterday European time!) by the Göttingen Genomics Lab. They say: 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 … Continue reading
Thanks to Konrad Paszkiewicz from University of Exeter for this SNP-based analysis of the 3 E. coli outbreak genomes. He used MUMmer to compare each complete E. coli genome available in NCBI to the Ec55989 chromosome, and identify single nucleotide polymorphisms (SNPs, i.e. substitution mutations, where one DNA base is swapped for another). He ignored … Continue reading
BGI has now formally released their data, including Illumina reads, under Creative Commons 0 (CC0) 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 … Continue reading
Now that the outbreak has been firmly traced back to sprouts, attention is turning to how the sprouts were contaminated in the first place. The initial assumption was that this would be a classic case of contamination with E. coli via feces from cows or other livestock, however in this case it is more likely … Continue reading
The Health Protection Agency in the UK has released a third E. coli O104:H4 genome from the German outbreak, strain H112180280. 454 reads and scaffold are available here: http://www.hpa-bioinformatics.org.uk/lgp/genomes (BGI has also released an updated assembly but not sure yet how it was done.) It contains a 73 kbp scaffold with matches to the other … Continue reading
