Question: SSPACE option (-k and -a) for scaffolding
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2.2 years ago by
Picasa390 wrote:


I am trying to play with SSPACE's parameters, especially the -k and -a option.

According to the manual:

-k  Minimum number of links (read pairs) to compute scaffold (default -k 5, optional)

-a  Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.7, optional)

But I am not sure to understand those 2 options. If someone has better and clear explanation, it will be helpful.


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