454 Assembly viewer

[pr0t3us]

Hi to all,
I'm new here and I find this forum very usefull!!
I work with 454, and now we start to have some shotgun sequencing project.
My problem is visualizing the newbler output. I'd like to have a web structure for visualizing the assembler output, the aligned reads and the scaffold structures...

I'm thinking about genome browser, but I fear that it will be too slowly for managing large amount of data....

Have you some experience with this problem ?? In your opinion, Genome Browser can be used for this purpuse? Have you some ideas ??

Thank you in advance

Alex

[Vincent]

I am using EagleView to view 454Contigs.ace. It is very fast on my XP machine (with 2 GB Memory).

Newbler output file 454Scaffolds.txt contains all the alignment information of contigs, but not individual reads.

Cheers,
Vincent

[glacerda]

I think that if you have a very high coverage Gbrowse won't be good. But if you test it and find it's ok, please tell us If you do, use the adaptor Bio DB SeqFeature Store (for versions of gbrowse >= 1.69). It's faster than the usual Bio DB GFF.

I myself currently use consed for viewing the ace file, but I think that you want it to be online, right?

Another option would be to condensate the read coverage in an wiggle histogram and plot it in gbrowse. In this case, you will lose part of the information carried by the positioning of reads.