COST Action TD1303
European Network for Neglected Vectors
and Vector-Borne Infections
www.eurnegvec.org
Training school: Next-generation sequencing tools: from sample to bioinformatics
Dates: 16-20 March 2015 (5 days)
Venue: Coda-Cerva (Veterinary and Agrochemical Research Centre)
Address: Rue Groeselenberg 99, 1180 Brussels, Belgium
Invited speakers (trainers):
 Willie Weir (University of Glasgow)
 Muriel Vayssier-Taussat (INRA, Maison Alfort)
 Jean François Cosson (CBGP Unit, INRA, Montpellier)
 Christophe Klopp (INRA, Toulouse)
 Steven Van Borm (CODA-CERVA)
Local organizers:
 Laetitia Lempereur
 Marcella Mori
Training days
Sessions will be held from Monday March 16th to Friday March 20th. As stated above, the meeting point
for the very first day will be in front of the Institute at 8h30 AM. This will allow us to make all necessary
formalities to receive a badge to enter within the Institute. Please do not forget your ID card. Sessions will
start at 9h00 sharp and will end by 5h00 PM. The training school will end on Friday at 3h30 PM to allow
participants to take their flights. Two coffee breaks are foreseen and the lunches will be between 12h30
PM-1h30 PM.
AM: 9h00 to 12h30
PM: 13h30 to 17h00
Programme:
Day 1 (Monday, 16 March 2015)
Chairs: Marcella Mori and Laetitia Lempereur
Room: RO_UK_Auditorium
Programme:
 AM: General introduction on NGS tools (Steven Van Borm):
o Tools description
o Sample selection and quality
o Data: structure, quality and format
 PM: Possible applications of NGS tools:
o Bacteria (Muriel Vayssier-Taussat, JF Cosson)
o Parasites (Willie Weir)
o Viruses (Steven Van Borm)
Day 2 (Tuesday, 17 March 2015)
Chair: Steven Van Borm and Marcella Mori
Room: Building C
Programme:
 Practical works: Preliminary steps for sequencing and quality control using Illumina nextera
preps”
o quantification and quality control of DNA sample
o preparing libraries using nexteraXT workflow
o QC of libraries using agilent bioanalyser
o quantification of libraries using real time PCR
o preparing a pooled library & re-run QC & quantification on the pool.
Day 3 (Wednesday 18 March 2015)
Chair: Laetitia Lempereur
Room: RO_UK_Bacteriolgy
Programme:


AM: introduction to scripting (command line and Perl) (Willie Weir)
PM: basic scripting to prepare NGS for analysis (trimming primers, collapsing reads, finding
motifs, regexs etc) (Willie Weir)
Day 4 (Thursday 19 March 2015)
Chair: Marcella Mori
Room: RO_UK_Bacteriolgy
Programme:
 AM: -Introduction to RNAseq: introduction and practicals (Christophe Klopp)
 PM: -Summary of 454 sequencing and parasite metagenomics: introduction and practicals (Willie
Weir)
Day 5 (Friday 20 March 2015)
Chair: Laetitia Lempereur
Room: RO_UK_Bacteriolgy
Programme:


AM: RNAseq and 454 sequencing and parasite metagenomics: practicals (Willie Weir and
Christophe Klopp)
PM: Short ppt presentations of NGS and bioinformatics application within trainee’s research work
-Discussion and Conclusion: NGS’ future and criticism