New scaffolds for two E. coli outbreak genomes

Two new assemblies of the German E. coli outbreak strains were released today, one from BGI (452 scaffolds/contigs; Illumina Hiseq paired end, 500bp inserts) and one from HPA (13 scaffolds, 454 mate pair). This is how they compare, to each other and to reference genomes for Ec55989 (EAEC E. coli chromosome), Shiga-toxin producing phage VT2, pO186A (EAEC aggregative adhesion plasmid – detail here), and IncI plasmid pEC_Bactec (carrying blaCTX-M beta-lactamase).

Scaffolded assemblies of BGI (TY2482) and HPA (H112180280) E. coli outbreak isolates, mapped against reference sequences using BRIG.

The reference here is the HPA genome, and the near-completeness of the purple ring (BGI assembly) shows that the two assemblies contain nearly all the same sequences. Any differences could be real, but more likely they are assembly issues with both genomes.

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