The satsuma toolset seems very useful. I'm trying to improve contiguity by mapping scaffold-level assembly of species 1 to chromosomes in reference genome of species 2. I'm not sure whether to use Chromosemble or MergeScaffoldsBySynteny. It appears from the brief text on the website (http://satsuma.sourceforge.net/), I should be using MergeScaffoldsBySynteny, but both tools build superscaffolds. What is the difference between the two tools?
Hello,
The satsuma toolset seems very useful. I'm trying to improve contiguity by mapping scaffold-level assembly of species 1 to chromosomes in reference genome of species 2. I'm not sure whether to use Chromosemble or MergeScaffoldsBySynteny. It appears from the brief text on the website (http://satsuma.sourceforge.net/), I should be using MergeScaffoldsBySynteny, but both tools build superscaffolds. What is the difference between the two tools?
Thanks.