Hybrid sequencing assembly visualization

[tjahns]

Hi,

I'm working on a genome project where a primary assembly was computed with 454 GS de novo Assembler ('Newbler') and later enhanced with Sanger reads to close some simple gaps.

For the secondory assembly, Gap4 was used with the reads from the Sanger sequencing and the contigs from Newbler as as plain Fasta-sequence files input.

Is there some way to retrieve a visualization that shows the mapping of both Sanger and 454 reads vs. the contigs from the secondory assembly?

Apparently the best start would be the Consed .ace file produced by Newbler?

Greetings, Thomas

[sklages]

Hi Thomas,

using the newbler ace file is a good starting point.
Using a current version of consed [1], you can assemble your sanger
data on top.

For visualisation you can use consed itself or you might use the
hawkeye viewer [2] from the AMOS package.

[1] = http://bozeman.mbt.washington.edu/consed/consed.html
[2] = http://amos.sourceforge.net/hawkeye/

Hopefully this was what you are looking for

Sven

[BaCh]

Hi Thomas,

I'd start a bit differently: in a first step, use both the Sanger and the 454 reads together in a hybrid assembly. Newbler can do this, Velvet, MIRA and others (the last one being a shameless plug).

To your question: the "template display" of gap4 can also be used to visualise reads mapped to your contigs ... it might just be a bit slow for projects with 454.

Regards,
Bastien

[tjahns]

Perhaps I should specify my question a bit more: the hybrid assembly is given and I am not in a position to modify it (unless I can show it's got too many errors by the inspection I'm intending).

So I'm not currently planning to recompute the assembly. Also my evaluation of assemblers like euler-sr and velvet showed me they don't compare favourably with Newbler. Therefore I'm sort of hesitant to retry the complete assembly with another program.

What I would like to do is to view the mapping of both 454 and Sanger reads for the Contigs produced with gap4. Thus I would like to sort-of replace the 454 contigs mapped to the secondary contigs with a mapping of 454 reads to secondary contigs.

[Theon]

Hi, Thomas
I am working on a similar hybrid assembly with both 454 and Illumina reads.
As far as I understand, you want to view how the raw data from both the 454 and Illumina aligns against the assembly?
I have been using Mosaik which enables the this alignment and gives you a resulting .ace file which I then view with Eagleview.
You would however need the raw data files as input while using the assembly as reference.
Hope this helps.
Theon

[sklages]

I think you need to do some recomputing ...

e.g.

- write fasta of contigs of your complete assembly
- align your 454 data against this backbone using the current consed/cross_match (add454Reads.perl)
- assemble the sanger data ("Sanger reads to close some simple gaps") on top; they should align to where they belong
- remove the contigs backbone

The assembly should now look like the secondary assembly.

Now you can use consed and its tools to see alignments, chromatograms/flowgrams etc.

Or you can use the above mentioned hawkeye to visualize the mapping of your reads.

All these need some proper installation of consed and AMOS ..

Or maybe you can use mira as mentioned by Bastien.
AFAIK mira can use your contig(s) as a backbone to align all 454/sanger against. This will also make sure that your assembly layout remains unchanged.

I'd prefer other assemblers over newbler ...

Just some ideas ...

Sven