Depth viewer for 454 data.

[gilly]

Hi all.

This is my first post. Can I start by saying what a wonderful forum this is and I hope to become an active member of the community.

I run a 454 production facility in Cambridge UK. Our job isn't to study the data but rather to make sure that the assembly is in a good enough state that the researcher can. The majority of the projects we do are 3 kb jump paired end and we have found that this protocol, although very good overall, does have some peculiar anomalies such as massive spikes of depth (up to 30,000).

Therefore what would be extremely useful to us would be an overall depth plot of an assembly that we could then update as new data was added. This wouldn’t need to show the base composition of the data but just a graphical representation of the assembly over all.

Does such a program exist?

Regards.

[flxlex]

454AlignmentInfo

Have you looked at the 454AlignmentInfo.tsv file coming with the newbler output? It lists, for all contigs, for each base, the read depth, quality and signal intensity. Using graph software (for example R, I use Origin) you can plot the depth for one or a large number of contigs.

Hope that helps!

[gilly]

Cheers for the info flxlex. Prefect!