News and Events

International simulation of VTEC outbreak

posted Jan 15, 2018, 12:37 PM by Mirko Rossi   [ updated Jan 15, 2018, 12:38 PM ]

An international simulation of VTEC outbreak using the INNUENDO platform designed and developed by our consortium
will be held during the weeks 6th and 7th of 2018 (i.e. from 5th to 18th of February 2018).
During this simulation representatives of ECDC, EFSA, EURL VTEC (Istituto Superiore di Sanità, Roma, Italy), Finnish National Public Health Authority, the Finnish Food Authority, the Estonian Veterinary and Food Laboratory, the Latvian Institute of Food Safety, Animal Health and Environment, Instituto Nacional de Saúde Dr. Ricardo Jorge Portugal, Luxembourg Institute of Health, Bundesinstitut für Risikobewertungand, and Austrian Agency for Health and Food Safety will performed in silico phenotype prediction of the pathotypes, and clustering analyzing using wgMLST on a limited set of E.coli strains using the tools implemented in our consortium, simulating a real-time use of the platform

Streaming of the Summer Course in ”Genomics in foodborne pathogen surveillance and outbreak investigation”

posted Jun 21, 2017, 8:51 AM by Mirko Rossi

The symposium day of the summer course un "Genomics in foodborne pathogen surveillance" 12th July 2017 can be followed live in streaming through the following link: Live stream 12th July

The program of the day can be accessed here

Nature Microbiology Community

posted Mar 20, 2017, 6:34 AM by Mirko Rossi

We have been asked by the manager of the “Nature Microbiology Community” to "tell the story" behind INNUENDO in the Nature Microbiology Community. You can find our stories in the Nature Microbiology Community blog.

chewBBACA - comprehensive and highly efficient workflow for a Blast Score Ratio Based Allele Calling Algorithm

posted Mar 15, 2017, 1:13 AM by Mirko Rossi   [ updated Mar 15, 2017, 1:14 AM ]

The novel allele calling algorithm chewBBACA have been developed by João André Carriço @jacarrico group. 
It is a comprehensive and highly efficient workflow for a Blast Score Ratio Based Allele Calling Algorithm. 
The algorithm is developed in python and its source-code is freely available.

A quick usage guide covering installation and software execution is available at
A complete description of the algorithm usage and parameters can be found in

It is currently comprised of three main modules: Schema Creation, Allele Calling and Schema Evaluation.

INNUENDO at ABPHM meeting 2017

posted Mar 15, 2017, 1:08 AM by Mirko Rossi   [ updated Mar 15, 2017, 1:08 AM ]

João André Carriço @jacarrico will be at the ABPHM meeting 17-19 May 2017, Wellcome Genome Campus, Hixton, UK

INNUca v 2.3 - our software pipeline for automatic QA/QC measures of FastQ reads

posted Mar 15, 2017, 1:05 AM by Mirko Rossi   [ updated Mar 15, 2017, 1:09 AM ]

The new version of INNUca is available at
This new version includes several new features:

- "True estimation module" - very fast estimation of chromosomal coverage
- Possibility to include PEAR 
- Possibility to use either SPAdes v3.9.0 or v.3.10.1

INNUENDO at ECCMID 2017 - ESCMID Networking Corner

posted Mar 15, 2017, 1:00 AM by Mirko Rossi

As every year, ESCMID will arrange a networking corner at ECCMID in Vienna, for providing an opportunity for ECCMID participants to get information about the increasing number of study groups, networks, organizations, collaborative centres and project groups active in the fields of clinical microbiology and infectious diseases and to facilitate information exchange and networking. INNUENDO will be present with a poster.

Onsite, the ESCMID Networking Corner will be centrally located with a leisure area with tables and chairs for informal meetings and discussions adjacent to the ESCMID World. The onsite networking corner will be open during the entire meeting. Online, it will be reachable via the congress app, the information kiosks and on the ESCMID website in the eLibrary ( from Friday, 21 April 2017 onwards.

For further information about ECCMID 2017, the scientific and educational programme, congress registration and hotel reservation, please visit the congress website at All posters presented in previous years are available on the ESCMID website here

INNUca - our software pipeline for automatic QA/QC measures of FastQ reads

posted Jul 11, 2016, 3:39 AM by Mirko Rossi   [ updated Jul 11, 2016, 3:40 AM ]

In the epidemiological surveillance of food-borne pathogens (FBP) using whole-genome sequencing (WGS) data, the raw read sequencing data (and downstream derived data) need to be properly handled and interpreted in order to be useful for public health action, i.e., allow meaningful linkage of cases, and subsequently timely detection of clusters and outbreaks. As such, it is critical to evaluate the potential existence of technical errors occurring in sequencing and downstream analyses (whose effect is still unclear) and further minimize them by setting up careful QA/QC measures. In this regard, the development of software pipeline for automatic QA/QC measures ultimately aims at producing consistent high-quality comparable genomics data. Such data can be subsequently processed through plenty of downstream analytical strategies (i.e. gene-by-gene, FCST, SNPs) depending on the pathogen under epidemiological surveillance and on the type of analysis (e.g. fast clustering analysis for real-time outbreak investigation or a population genetic study for long-term prospective epidemiological surveillance).

We developed an automatic bioinformatics pipeline INNUca - INNUENDO Reads Control and Assembly – for performing QA/QC measures on sequencing. The software pipeline was conceived to be fully flexible, portable and pathogen-independent, thus potentiating its suitability for systematic processing of large numbers of files and minimizing inter-laboratory variation.

The software is available for downloads at


posted Apr 25, 2016, 2:30 AM by Mirko Rossi   [ updated Apr 26, 2016, 2:07 AM ]

University of Lisbon (Técnico Lisboa; Facultade de Medicina; Facultate de Medicina Veterinaria; Facultade de Ciências) and Universidad del País Vasco/Euskal Herriko Unibertsitatea had agreed on a inter-institutional agreement for exchange students within Erasmus + programme.



Subject area code

Subject area name

Study cycle

Mobility period




Biological and related sciences


2 x10 months

(Total 20 months)




Biological and related sciences (microbiology)


2 x 10 months

(Total 20 month)

Applications for nominated students must reach the receiving institution (both 2nd cycle) by

UL: Autumn term (October) – 15th May till 15th June; Spring term (January) – 15th October till 15th November 
UPV/EHU: Autumn term (October) – May 31st; Spring term (January) –October 31st

Please contact your institution for more information.


posted Apr 22, 2016, 9:19 AM by Mirko Rossi   [ updated Apr 25, 2016, 2:30 AM ]

João André Carriço @jacarrico was present at the ECCMID 2016 9-12 April 2016, Amsterdam, Netherlands.

You can see his presentation in Slideshare (

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