Scaffolding mira contigs

[Mona]

hi,
I am doing de novo assembly of 454 reads, i have got the contigs using mira assembler, now i want to do the scaffolding of those contigs, the scaffolding tool that comes with mira is bambus but it uses reference genome for scaffolding, some one please suggest me how to perform the scaffolding of the contigs without having reference sequence also my data is not paired end.

[mhampton]

What organism?

I might be in a similar situation. What organism(s) are you studying?

[Mona]

I m studying genome of a spirochete(bacterium).
So what are you going to do for this?

[sklages]

For scaffolding, which is "just" an ordering of contigs, you will either need a reference genome or paired-end data ... how do you want to order contigs without having any information about their relationship?

cheers,
Sven

[Mona]

yes this is what i m also wandering.. but from where can i get the reference genome? When i blast my reads in ncbi.. i m not getting any reasonable similarity with any genome..
how do the people used to perform assembly and scaffolding jobs when they started doing this, without having any reference genome?

[sklages]

how do the people used to perform assembly and scaffolding jobs when they started doing this, without having any reference genome?

They used paired-end data ;-)

... and then closed gaps via PCR if necessary ...

Sven

[Mona]

hmmm.......