Goldrush for PacBio or ONT + PacBio about goldrush HOT 3 CLOSED

Thanks for your interest and sorry for the delayed response.

GoldRush has been tested on just PacBio Hi-Fi human data. GoldRush assembles PacBio Hi-Fi human data well in our experiments (high base quality and single digit MB NGA50) but the genome assemblies do not reach the level of contiguity of ONT genome assemblies due to the lower read length, which affects the scaffolding algorithm used.

I'm not sure if you have Hi-Fi or CLR but If you were to use GoldRush on PacBio Hi-Fi data, you will have to change the m parameter to the library sized used in generation of the PacBio Hi-Fi data.

Right now, GoldRush does not support hybrid data out of the box. It is possible to manually generate the golden path with PacBio data and scaffold with ONT though we have not explored how much coverage is needed for optimal scaffolding. We are looking to add the option for out of the box hybrid genome assembly in a future update.

60X and 40X should be sufficient coverage to run the GoldRush pipeline.

Regards,
Johnathan

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Thank you for all the details! Very helpful

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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 GoldRush!

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