State-of-the-art France GBF-Toulouse Sequencing Team BAC selection and Finishing Murielle Philippot Pierre Frasse Genome Assembly Vincent Cahais Sana Hakim Simo Zouine Infrastructure and involvement of Bioinformatic Plateform INRA- Toulouse

–1 seule banque pour obtenir simultanément des séquences de type shot-gun et L-PET –Séquences de L-PET de plus grande taille, ~100 bases pour chacune des extrémités

State-of-he-art France GBF: 12 Runs –12 runs 3kb home-made different library + 8 runs Shotgun planned for July –August lack of DNA) – sequences (3 runs) WUR: 27.5 Runs – séquences –15 runs Shotgun –6 runs 3kb –6.5 runs 20k Italy: 2 Runs – séquences –1 runs 3kb –1 runs 20kb

Mean sequence length: 400 – 500 nt Mean sequence quality: 25 – 30 Shotgun gives: - longer reads (550 nt) - higher frequency of long reads Chloroplast and mitochondria genome contamination: - estimated very low (1600 – 1800 / 500k reads corresponding to 1 run) The ration of 2 runs for 1 x coverage has been slightly over-estimated Conclusions

1 run 454 sequencing of the 8 or 20 kb new PET libraries BAC-end sequencing of the sheared library ( clones; 5-6 x) Whole Genome draft assembly with non Newbler assemblers Suggestions - Questions