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
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