Re: [wgs-assembler-users] using contigs from sanger shotgun in the assembly.

[Walenz, B. <bw...@jc...>]

Q2: No.  Long a desired feature, but never enough resources to implement it.

Q1: If you load these preassemblies as reads, they will never be broken up.
What should then happen is the 40x of Illumina reads will have containment
overlaps to the preassemblies, and, hopefully, each preassembly will form a
single unitig with gobs of Illumina reads (with mates) inside it.

I tried something similar for one of our Salmon assemblies.  It kind of
worked, but the repeats were so complicated that it could have easily
assembled a chimeric repeat.

Careful!  If you have any unique sequence at the end of the preassembled
repeat, this 'read' will look like a normal non-repetitive read and you'll
lose all the other copies of the repeat.

An alternative approach would be to use the preassemblies to remove repeat
reads from the assembly, then use a gap filler to walk through the resulting
scaffold gaps.

b


On 10/25/13 1:20 PM, "Mayank Mahajan" <may...@ic...> wrote:

> Hej Brian,
> I have preasembled sanger data from the repeated regions in my
> assembly. The repeats are too many and pretty messy to handle
> manually. I know that I can provide them to the assembler as normal
> fragments using fastaToCA.
> 
> Q1.Is there some way to give really high priority to these
> contig/unitig size fragments as each one of these reads is much high
> quality than the Illumina reads which I use with 40X coverage.
> 
> Q2. Is it possible to do backbone assembly.
> 
> Regards,
> Mayank
> 
> 
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