circular genome contigs not scaffolded properly

[kmnip]

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-.

[github-actions[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in ABySS!

[github-actions[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in ABySS!

[github-actions[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in ABySS!

[vlad0x00]

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