Scaffolding with Newbler?

[dan]

Hi,

We have an existing assembly that we'd like to scaffold using BAC end sequences. Since we've had good experiences with Newbler, we thought we could try to use that. However, Newbler (at least version 2.8) doesn't seem to allow us to open an *existing* (non 454) assembly and combine it with the BES... Also, it doesn't seem to have a way to specify the insert size (and our contigs are much shorter than BACs).

a) Can Newbler do this kind of job?
b) Which other scaffolders would you recommend?


Cheers,

[flxlex]

Newbler is not a stand-alone scaffolder. Also, it cannot be told the insert size. Instead, it determines the library insert distribution based on placement/mapping of the mates in the contigs it builds. So, newbler needs to be able to build contigs from your data that are long enough for a sufficient number of mates to map to the same contig.

Looks like you need a stand-alone scaffolder...