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Add support for --plasmids and --meta flye flags #10

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dfornika opened this issue Nov 28, 2023 · 2 comments · Fixed by #11
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Add support for --plasmids and --meta flye flags #10

dfornika opened this issue Nov 28, 2023 · 2 comments · Fixed by #11

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@dfornika
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dfornika commented Nov 28, 2023 •
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flye supports two flags (--plasmid and --meta) that aren't directly exposed in dragonflye. Use dragonflye's --opts flag to optionally pass them through.
@dfornika
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dfornika commented Nov 28, 2023 •
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It appears that the --plasmid flag has been deprecated as of release 2.9:

https://github.com/fenderglass/Flye#flye-29-release-20-aug-2021

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The --meta flag is advised if we 'expect highly non-uniform read coverage'. The author of flye cautions that "some graph procedures will be less aggressive, which can decrease the contiguity of a single genome assembly".

https://github.com/fenderglass/Flye/blob/4fc23c4f53c384468735ea2443ce8df465e02f63/docs/FAQ.md?plain=1#L33-L39

@dfornika dfornika mentioned this issue Nov 28, 2023
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Add support for flye --meta flag BCCDC-PHL/dragonflye-nf
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