Questionnaire on foodborne viruses Next Generation Sequencing

Welcome to the “Questionnaire on the application of Next Generation Sequencing technology”. This questionnaire aims to get a view of the NRLs capacity of NGS, the actual needs of the NRLs and the interest in participating in a working group on NGS organized by the  EURL for Foodborne viruses.

Contact information
 
Laboratory name
 
Country
 
Contact person(s) for this enquiry
 
Email address
 
Technical questions
 
Q1: In your role of NRL, which of the following NGS activities do you perform?
 
WGS
Amplicon NGS
Metagenomics sequencing
Bioinformatics analysis
Q2: If replied "not performed" to at least one of the questions in Q1, please specify why.
 
If replied "not performed" to all options in Q1, please continue to question 19.
 
Q3: If you answered positively to at least one of the options in Q1, what is your purpose of using NGS in your NRL?
Q4: If performing NGS, on which viruses?
Other viruses
 
Q5: What concept do you use for nucleic acid extraction for sequencing?
Other concept
 
Q6: How do you assess the purity of the nucleic acid extracted before sequencing?
Q7: How do you estimate the concentration of the nucleic acid extracted before sequencing?
Other method
 
Q8: Which protocol do you use to prepare the library for sequencing?
 
Q9: How do you evaluate the quality/concentration of the prepared library before sequencing?
Other Method
 
Q10: Please specify which NGS platforms you use and/or are used by the lab/company to which the activity is outsourced
Other Platform
 
Q11: What parameters do you use to evaluate the quality of sequence data (reads and/or contigs)?
Other Parameter
 
Q12: Where is NGS data analysis performed?
Q13: Which approach do you use for data analysis?
Q14: Do you perform cluster analysis?
Q15: If answered yes to Q14: How do you perform cluster analysis?
 
Q16: Have you performed benchmarking to compare protocols?
Q17: If Yes, please specify the methodology
Q18: Have you ever participated in NGS-based proficiency schemes for virus?
If Yes, please specify
 
Q19: Are you interested in participating in Proficiency Tests organised by the EURL?
Q20: If Yes, for what activities?
Other activities
 
Q21: Has your NRL staff received training on NGS?
Other Training
 
Q22: Would you be interested in participating in training on NGS organised by the EURL?
Q23: If Yes, please specify which part of NGS training you are interested in?
Other Training
 
Q24: Which approach would you prefer for training on NGS data analysis?
Q27: Would you like the EURL to organise a working group on NGS for the NRLs?
Q28: What should such working group focus on?
Other Suggestions
 
Q29: Additional comments
 
 
Reviewed 2019-04-29