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Old 10-13-2010, 01:58 AM   #1
nicolallias
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Location: France

Join Date: Jan 2010
Posts: 23
Default gsAssembly (Newbler) de novo behaviour, inputs and outputs

Hello there,
It appears that the content of the ACE file is quite inconsistent with the fasta files content and the 454NewblerMetrics file:
Sometimes, the fna files are empty, 454NewblerMetrics has no contigs nor isotigs but...
The corresponding ACE will have a hundred contigs/isotigs with a mean depth of 10 000 and minimum size of 120.
Looking into the ace file show that these sequences are fulled with "*".

So I wonder: is the ace file a temporary (unfiltered) one ?

Another point: it seems that running a de novo assembly starting from fasta and not sff improve the assembly quality (less "*" in the sequences)

Anyone has seen that ? Is there some Newbler options to use for fixing this ?
Cheers
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