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New analytical pipeline for the characterization of STEC from NGS data

EURL-VTEC has developed an analytical pipeline for the characterization of STEC from NGS data. The pipeline accepts both single and paired end raw reads and returns all the information related with the serotype, the MLST Sequence Type (ST) and the virulotype of the sequenced strain. The pipeline also does the trimming and the assembly of the reads producing the related outputs together with the QC in separate files. At the moment the pipeline (EURL_VTEC_WGS_PT) is visible to all the users of ARIES, our bioinformatic platform, under the “E. coli typing” menu. We are also setting up a web service to make the pipeline available also to all the other subjects who are not ARIES users that will be exposed on-line in the near future. We’ll keep you posted on the exact date through our "Focus on” feed.

The ARIES platform is also accessible through the E. coli Genomics section of the EURL website.

Published 31-05-2017 in Focus on , last update 31-05-2017

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