I am a little bit confused about using the related genome or reference genome.

When we have a reference genome, we can do alignment. Also we can do the assembly.

Can you give some more reason why a related genome can help to improve gene model ?

And if we do use a related genome, what kind of problems or caveats may occur there ?

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    $\begingroup$ can you please be more specific, like what species you have in mind and if you are talking about RNA or DNA? $\endgroup$ – Michael Kuhn May 14 '14 at 7:16

Why a related genome helps:

1) Alignment of the reads first and assemble next. 2) The gene-space is already predefined ( the genes and their co-ordinates are already known), so if your assembly is fragmented or missing a portion of the gene information, that can be accomodated with reference genome.

Limitations: Rather than assembling your own genome, you are forcing the reference genome to be part of your genome assembly. If at all, any differences are there, they are washed out, when you do a reference assembly.

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