Re: [wgs-assembler-users] coverage information for scaffolds/contigs

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

Hi, Christoph-

[Sorry, wrote this 16 hours ago and forgot to send]

Check out the 'fragmentDepth' utility.  It computes coverage, and outputs in
three different ways: coverage of each scaffold, a histogram of coverage (as
at the end of *.qc), and a fasta-like output of the actual depth of coverage
at each base in the scaffold.

I can't think of a reason it would fail on contigs, but I haven't tried it.

The posmap files should be capturing most of the important stuff from the
(agreed: very difficult to use) asm file.  If you can't get what you're
looking for out of the posmap files, we need to add to them.

b



On 8/8/12 6:20 AM, "Christoph Hahn" <chr...@gm...> wrote:

> Hello CA developers and experts,
> 
> I have just finished my first big 454+illumina hybrid assembly using CA7
> and I am about to assess the result now in comparison to purely illumina
> based assemblies.
> 
> One question there: What is the easiest way to get coverage information
> for the scaffolds, contigs, unitigs in the *.scf.fasta, *.ctg.fasta,
> etc. files? I figured, that it is possible to calculate it manually
> using the information in the *.posmap.frgscf and *.posmap.scflen files
> (in case of scaffolds). I guess, the information is also in the *.asm
> file, but I am having problems reading/parsing the file.
> Is there an easy way you can think about?
> The reason, why I want to do this is that I want to bin the
> scaffolds/contigs based on coverage, GC-content and length.
> 
> Any ideas are highly appreciated, thanks!
> 
> Much obliged,
> Christoph
> 
> University of Oslo, Norway
> 
> 
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