Please report
CentOS Linux release 7.4.1708 (Core)
I am trying to assemble a circular genome. I end up with two contigs that are not scaffolded in one piece.
Here is my -6.dist.dot:
digraph dist {
graph [k=117 s=200 n=10]
"0+" -> "1-" [d=-105 e=11.8 n=136]
"0-" -> "1+" [d=-69 e=25.5 n=29]
"1+" -> "0-" [d=-105 e=11.8 n=136]
"1-" -> "0+" [d=-69 e=25.5 n=29]
}
Although there is ample read support between the two contigs, no scaffold is generated from these distance estimates because they are ambiguous.
I can set n=30 in abyss-pe to skip the less-supported distance estimates to create a single scaffold.
Can abyss-scaffold have an option to detect cycles and scaffold accordingly? For the example above, I would expect a scaffold with the path 0+,1-.
Please report
abyss-pe versionlsb_release -dI am trying to assemble a circular genome. I end up with two contigs that are not scaffolded in one piece.
Here is my
-6.dist.dot:Although there is ample read support between the two contigs, no scaffold is generated from these distance estimates because they are ambiguous.
I can set
n=30inabyss-peto skip the less-supported distance estimates to create a single scaffold.Can
abyss-scaffoldhave an option to detect cycles and scaffold accordingly? For the example above, I would expect a scaffold with the path0+,1-.