why consed after Newbler

[nicedad]

Hi everyone,
I'm just getting my feed wet with NGS thus my questions usualy appear to be very naive.

My question this time is, why one should use another tool i.e. CONSED to deal with the result of an assembler i.e. Newbler even though the later
does the trimming and removes the primers?

thanx in advance.

[nickloman]

For viewing the assembly, designing finishing primers, joining contigs together etc.

It's not a required step if you want to just deal with the draft contigs.

Quite helpful though. You can use other viewers (Tablet, for example) for viewing the assembly if you prefer.

[nicedad]

For viewing the assembly, designing finishing primers, joining contigs together etc.

Necloman, thanks a lot for the replay. could you plese advise, why one should
join the contigs to gether since we already get the consensus?

You can use other viewers (Tablet, for example) for viewing the assembly if you prefer.

really nice tool will check it

[nickloman]

Necloman, thanks a lot for the replay. could you plese advise, why one should
join the contigs to gether since we already get the consensus?

Well, presumably your assembly is in fragments.

In some circumstances you may want to join those together through some finishing experiments, perhaps there's a region of particular interest and it is split in two by a repeat.

If you are lucky enough to have the assembly in a single contig then you don't need to do this, but it's pretty unusual!

[nicedad]

Do you mean that contigs must be joined to analyse a cDNA?
if yeah, how to join them if the data are many Mbs?

best,

[westerman]

cDNAs are usually from mRNA (transcripts of protein expression) and thus are short, on the order of 1000 base contigs. A 454 project using Newbler with the '-cDNA' flag is excellent for creating complete contigs that can not and should not be further merged. We use Blast2Go to annotate our 454 runs.

On the other hand, a whole genome shotgun assembly will almost always produce many contigs which can then be merged together into chromosomes (at least in theory) or at the very least into longer contigs. Using Consed or other tools will help scaffold and merge those contigs together or at least tell you what further work to do in order to get good merging.

How to join them together? Usually requires more sequencing. Either directed or random. And much hoping that repeats don't get in the way. "Finishing" is a tough human-labor-requiring problem -- that is why there are so many unfinished genomes out there.

[nicedad]

nickloman, westerman, thanks for your patience!