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

[Christoph H. <chr...@gm...>]

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