Re: [Denovoassembler-devel] Confused about coding -- 500k phiX simulation still fails

[Eccles, D. <dav...@mp...>]

From: Sébastien Boisvert [mailto:seb...@ul...]
> I think you generated too few reads.
> That is why it fails.
> You need to get the peak coverage at least above 20.

Okay, so I used the VirtualNextGenSequencer to create 500,000 reads, which
has a substantially higher coverage:

http://pastebin.com/18SwshYE

It actually registers as having a peak now, which is nice, because it can
then proceed with the assembly. The statistics are still a little odd,
finding a peak at 1415 (neighbourhood counts 58,52,70,74*,56,72,68) when 2862
has a higher count (70,54,72,82*,56,50,52), as does 2873
(56,58,60,76*,64,76,64), but I'll put that down to smoothing -- it's close
enough.

So now that I've muscled my way past the coverage, the assembly should be a
breeze:

http://pastebin.com/xJJ9yycT

... or maybe not. It [still] looks like it's failing on seed creation.

Would it make sense to include a coverage calculation in the seeding tests
done by the workers (SeedWorker.cpp)? What happens if a vertex (with >5
coverage) has a parent that has 1 edge in, one edge out, but the coverage of
that parent is below 5?

-- David