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circular genome contigs not scaffolded properly #385

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kmnip opened this issue Jan 11, 2022 · 4 comments
Open
2 tasks

circular genome contigs not scaffolded properly #385

kmnip opened this issue Jan 11, 2022 · 4 comments

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@kmnip
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kmnip commented Jan 11, 2022

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-.

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github-actions bot commented Feb 3, 2022

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 github-actions bot added the stale label Feb 3, 2022
@vlad0x00 vlad0x00 removed the stale label Feb 3, 2022
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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 github-actions bot added the stale label Feb 24, 2022
@lcoombe lcoombe removed the stale label Feb 24, 2022
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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 github-actions bot added the stale label Mar 17, 2022
@vlad0x00 vlad0x00 removed the stale label Mar 17, 2022
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