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That's an interesting question. Could you post the assembly graph (the extended.fastg file) or the visualized version of the graph here so that I can understand your request better? |
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Hello and thanks for supporting this tool, its been working great.
I am working on mtgenome assembly from reads for some organisms for which we expect the mtgenome to be linear. GetOrganelle will usually perform as expected, and "fail" to circularize the assembly; this is fine, as the path generated seems to reflect the linear genome accurately.
Sometimes it "succeeds" at disentangling the graph, however, and generates a circular genome. I am guessing this is due to a spurious detection of overlap at the ends. The result is that the top path generated has the incorrect start and stop positions.
I am wondering if there is a way to force a linear assembly. I tried setting --disentangle-time-limit to 0 or 1 second, but it still circularized, not sure how.
Thanks in advance!
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