.branch operator triages barcode assemblies with sufficient number of contigs (>= 3) for trycycler. Assemblies with < 3 contigs does not attempt trycycler assembly and avoids all errors relating to this (#21).
43 can now focus solely on improving the trycycler method implementation)
Bunch of formatting
In this PR, each sample is handled by one of the following cases:
Enough contigs for trycycler, flye is better assembly (barcode03)
Enough contigs for trycycler, consensus is better assembly (barcode01)
Not enough contigs for trycycler, use flye assembly (barcode12)
In Case 1, some flye contigs are discarded to only retain chromosomal contigs before polishing and annotation (current select assembly implementation)
This PR introduces Case 3, where no contigs are discarded.
All flye-assembled contigs are polished and annotated etc. This is to prepare for revising the approach for #54. (The unicycler assembly is not considered as one of the good assemblies here, to change when revising.
.branchoperator triages barcode assemblies with sufficient number of contigs (>= 3) for trycycler. Assemblies with < 3 contigs does not attempt trycycler assembly and avoids all errors relating to this (#21).43 can now focus solely on improving the trycycler method implementation)
In this PR, each sample is handled by one of the following cases:
In Case 1, some flye contigs are discarded to only retain chromosomal contigs before polishing and annotation (current select assembly implementation)
This PR introduces Case 3, where no contigs are discarded.
All flye-assembled contigs are polished and annotated etc. This is to prepare for revising the approach for #54. (The unicycler assembly is not considered as one of the good assemblies here, to change when revising.
Output report and files on sharepoint