Re: [wgs-assembler-users] gap length

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

The length=20 gaps mean that the mate pairs claim the adjacent contigs
overlap, but no sequence alignment could be found.  The .asm file contains
the true (negative) gap length in the CTP message.

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=ASM_File
s#SCF_CTP

mea: The mean distance gives the predicted number of bases in the gap
between the contigs. It is measured from contig end to contig end. A
negative distance indicates that the contigs overlap (according to their
aggregate mate pairs) though their consensus sequences do not align. In the
FASTA representation of a scaffold, negative gap lengths are represented
arbitrarily by 20 N's.

b



On 11/11/13 1:07 PM, "Cristell Navarro"
<cri...@om...> wrote:

> Hi!
> 
> I'm looking for an explanation because my scaffolds have most of their
> gaps with length = 20. This means something in special?, Is this a
> minimal gap lenght that the assembler use for gaps of unknow length?
> 
> I hope you could help me with this issue, because I would like to submit
> my data to ncbi...
> 
> thanks in advance!
> 
> Cristell
> 
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