circular genome contigs not scaffolded properly #385
Description
Please report
- version of ABySS with
abyss-pe version
abyss-pe (ABySS) 2.3.1
- distribution of Linux with
lsb_release -d
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-.