An iterative assembly of the sort that you're describing is not yet
supported by ABySS. It is on the wishlist. I'd be interested to hear
from anyone that is using scaffolding software with ABySS contigs.
I have now tried SSPACE on a genome of 450 MB and it took about 2 days with contig extension and less than a day without. I had two fragment libraries (PE) and one jumping library (MP). I'm not sure how that will scale up with genome size. I was quite happy with the results from the quick look I've had so far.
Hope that helps a little
On Jan 11, 2011, at 09:17 AM, Zhang Di wrote:
How long will SSPACE finish a contig extension run for a typical large genome (such as 1G bp)? 1 day, 2 days, a week, or a month?
On Wed, Dec 15, 2010 at 4:54 AM, Andreas Sjödin <andreas...@gmail.com<mailto:andreas...@gmail.com>> wrote:
Hi Shaun and Nathaniel,
I have evaluated different scaffolding methods for bacteria genomes
where I can compare to a very close relative (finished genome). So not
exactly large genomes but I think same approach would work for larger
genomes too. The main reason I decided to go for a iterative process
is that I want to add external information (known genome structure
including duplication etc.) to my scaffolding runs, plus abyss had
some problem with my mate-pair data. I am finally using ABYSS contigs
as starting point together with other know information and I am then
doing the scaffolding iteratively in SSPACE and contig extension to
more or less close the genome. I also get similar results using BAMBUS
with ABYSS contigs as starting point. However, the combination of
ABYSS and SSPACE gives me most control of the process plus that I
don't need spend time to convert any files (like in other option as
BAMBUS or Velvet).
I am looking forward to have some similar interactive function in
ABYSS in the future.
Umeå Plant Science Centre
Department of Plant Physiology