Re: [wgs-assembler-users] Wrong GC-content and lower quality assembly

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

Hi-

I can't reproduce your gc content claim.  Looking in the code, the gc
compute will return an incorrect value if there are lowercase letters in the
scaffold sequence.  Can you check that your scaffold sequences have no lower
case?

Can you elaborate on what 'quality decreased' means?  Just shorter
assemblies, or validated against a reference incorrect regions?  What
parameters are you using?  What type of reads?

b



On 10/4/13 7:26 AM, "Mayank Mahajan" <may...@ic...> wrote:

> Hello,
>      I just downloaded the new wgs-assembler 4 days ago. The GC
> content reported by caqc.pl in the end is wrong. When I calculate GC
> using the XXX.scf.fasta file I get 3% higher GC content which is
> correct as verified using assemblers. Also the quality of assembly has
> decreased now as compared to the release from the  last month. I have
> tried different coverage and parameters but there are always these
> extremely sceptic regions with almost no coverage or too much coverage.
> 
> Warm Regards,
> Mayank Mahajan