Hi all,
for my diploma thesis I wanted to roughly describe how Newbler works. Reading the paper from Ewan Birney, he explains the de Brujin graph structure and says:
"The first assembler to exploit this technology was Roche's 454 assembler, Newbler, which adapted the scheme specifically to handle the main source of error in 454 sequencing—namely, ambiguity in the length of homopolymer runs."
Reading the paper from Margulies et al. from 2005 and its supplementary is mentioning an 'overlapper' module which performs an all-against-all fragment comparison. Sounds to me it uses an overlap graph.
Now I'm very confused about what it is actually using. Can somebody help me out?
Cheers,
Charles
for my diploma thesis I wanted to roughly describe how Newbler works. Reading the paper from Ewan Birney, he explains the de Brujin graph structure and says:
"The first assembler to exploit this technology was Roche's 454 assembler, Newbler, which adapted the scheme specifically to handle the main source of error in 454 sequencing—namely, ambiguity in the length of homopolymer runs."
Reading the paper from Margulies et al. from 2005 and its supplementary is mentioning an 'overlapper' module which performs an all-against-all fragment comparison. Sounds to me it uses an overlap graph.
Now I'm very confused about what it is actually using. Can somebody help me out?
Cheers,
Charles
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