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Old 03-12-2013, 10:34 PM   #2
kbradnam
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Location: Davis, CA

Join Date: May 2011
Posts: 53
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Overlapping reads can be merged to produce a single contiguous sequence which are called contigs. The first part of assembly is used to make contigs from reads. The next step is to see if some of these contigs can be joined together. This process is called scaffolding.

E.g. contig A and B might not overlap, but there may be a mate pair read that maps to contig A and the other read of the mate pair maps to contig B. Thus you can make one scaffold that consists of two contigs. In this case, the scaffold sequence would be padded with N characters to reflect the length of the unknown region between the two contigs. In some extreme cases a very large assembly of scaffolds, might contain a lot of Ns.

As for your second question, I suggest checking out the Assemblathon 2 pre-print that is currently on available on arxiv.org.

Regards,

Keith
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