Question --Incremental assembly using Nembler

[NSTbioinformatics]

Does anyone knows, what is the difference between the incremental assembly and all data together assembly by Newbler?

Does the incremental assembly take contigs from the previous assembly, rather than taking raw reads?

[flxlex]

With incremental assembly, reads are added to an existing assembly. But, they are not aligned to the existing contigs per se, but to the aligned reads, or more correctly, the contig graph of the aligned reads.

Hope that helps...

[NSTbioinformatics]

Thank you for you comments. I come out another question.

If the settings using on one of steps incremental assembly are changed, will Newbler redo the assembly on the previous assembly using new settings, or only use the setting for this step assembly?

For example.
First step,
newAssembly projectname
addRun 1.sff projectname
runProject -mi 95 -ml 50 -large -g -e 10 -v file projectname

The second step
addRun 2.sff projectname
runProject projectname
*****************
Will the new settings of assembly work on only file 2.sff or both of 1.sff and 2.sff?

Thank you very much.

[flxlex]

I am wondering the same thing and have actually posted the question to 454 without getting an answer.

But, when I think about what might happen, I guess the answer is no: I don't think the alignment/contig graph built during the first assembly (of the 1.sff file in your example) is modified because in the next phase you changed alignment stringency settings. I think the new settings only apply to the alignment of new reads (2.sff in your case).

But again, I am speculating here...

[NSTbioinformatics]

Thank you for your comments.

Maybe you are right. Then what happens when using new settings on the project again:
runProject -v file projectname

I assume it will work on both 1.sff and 2.sff.