Re: [wgs-assembler-users] surrogate

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

Hi-

The surrogates are included in contigs.  Searching against scaffolds +
degenerates (or contigs + degenerates) will use every assembled sequence.

A bit more:

Degenerates are either short low coverage unitigs or repeats that were not
placed.  Repeats that are placed are called surrogates, because they can
appear in more than one place.  We'll place the reads in the surrogates if
they can be placed uniquely (by a mate pair) otherwise, the contig where the
surrogate is placed will have zero read coverage in the posmap outputs.

b


On 11/21/13 4:22 PM, "Cristell Navarro"
<cri...@om...> wrote:

> Hi
> I was analizing the data that did not match in the scaffolds, first I
> looked for the degenerates, and now I would like to analize the Surrogate.
> 
> Where can I find a fasta file of the Surrogates contigs?
> 
> Cristell.
> 
> 
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