Diapositive 1 - Sol Genomics Network

peaceevenΒιοτεχνολογία

4 Οκτ 2013 (πριν από 3 χρόνια και 11 μήνες)

131 εμφανίσεις

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)


2 716 911 sequences (3 runs)



WUR: 27.5 Runs


22 486 227 séquences


15 runs Shotgun


6 runs 3kb


6.5 runs 20k



Italy: 2 Runs


1 366 781 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

(50 000 clones; 5
-
6 x)





Whole Genome draft assembly with non Newbler assemblers


Suggestions
-

Questions