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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
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Suggestion to Improve Assembly #47

Closed nsmt89 closed 3 years ago

nsmt89 commented 4 years ago

Cryptocoryne_nurii_1_Fast-Plast_Progress.log Hi, do you have any suggestion on improving towards completing this assembly?

Thank you

mrmckain commented 4 years ago

Could you sent me the other output files? Not the assembly but the other error/out files?

Thanks!

nsmt89 commented 4 years ago

Cryptocoryne_nurii_1_results_out.log Cryptocoryne_nurii_1_results_error.log Cryptocoryne_nurii_1_results_out.log Hi, I hope these are the files that you requested.

Thanks

mrmckain commented 4 years ago

Looking over these files, I might suggest using the option to reduce the total number of reds to ~2 million. Sometimes having too high of coverage causes the pipeline to keep breaks in the assembly.

nsmt89 commented 4 years ago

Is it by using --subsample option? If it is, where should I put it in the command line?

mrmckain commented 4 years ago

Anywhere is fine. All options have a specific ID, so order doesn't matter.