Assembling Solexa data using Newbler 2.3 Beta

[danbrami]

Has anyone attempted to de-novo assemble 100 bp Solexa reads with Newbler 2.3 beta yet?

I would be curious to know what other people think of their assembly outputs.

[nickloman]

Is Newbler 2.3 beta generally available?

[danbrami]

No. It isn't generally available but I assume a few other centers might have access to it.

[nickloman]

Right, I hadn't spotted it on the FTP. Does it have a short-read assembly mode then?

[danbrami]

Well, again, not quite;
I was assembling 100bp fragmentary Solexa reads; Newbler can handle reads as small as 50 bp; 'In the beginning', GS20 reads were approximately 100 bp in length as well so Newbler supports this size.

[nickloman]

Ah right. Have they made any changes to support Solexa reads? My guess would be that Newbler won't perform that well on non-454 reads as I would guess the software is optimised for the error rate and characteristics of the 454 reads. I realise it supports long ABI reads but I think they are supposed to be used sparsely.

[zhgai]

Who can make the new version of Newbler available?