Using MinION reads about tigmint HOT 6 CLOSED

Hello Raymond,
The Tigmint Makefile uses ARCS for scaffolding, which utilizes linked reads. Were you wanting to scaffold your assembly post-Tigmint with the MinION reads or linked reads?

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Hi Icoombe,
MinION data, I don't have linked reads. It seems that I can't rescaffold my assembly with MinION.

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Hi Raymond,
Although ARCS (which is the scaffolder used in the Tigmint Makefile) uses linked reads, you could look at using a scaffolder designed for long reads, such as LINKS (https://github.com/bcgsc/LINKS) after breaking your assembly with Tigmint.

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@asdcid didn't you also notice that TIGMINT seems to cut assemblies at homopolymers with MinION reads?

My guess here is that the homopolymer errors in MinION reads lead to dramatic-looking drops in coverage at one end of a homopolymer run (depends on how the aligner works, but they usually bunch all the bases up at one end or another), and that this might be throwing TIGMINT off.

We wondered if this is something that could be addressed by just adding in an expectation that one would see coverage dropoffs around homopolymers. (Also I this might be a separate issue).

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Which aligner did you use with your MinION reads, and have you tried Minimap2? It should be able to align through simple sequence repeats. You may want to try increasing the chaining parameter -r.

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This issue has been automatically marked as stale because it has not had any recent activity. It will be closed in 7 days if no further activity occurs. Thank you for your interest in Tigmint!

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