I have ONT only Shasta and Flye assemblies and dbg2olc and Masurca hybrid assemblies. I was wondering if there is a suggested strategy for merging them all with quickmerge. Is it as simple as cat the long-read only and cat the hybrid assemblies together and then provide the two files to quickmerge?
Also regarding this helpful tip:
For optimal merging results, identify the major misassemblies (especially translocations and inversions) in the component assemblies and break the contigs at such misassembly boundaries. Alignment of the component assemblies to the merged assembly may help to identify such assembly errors because a specific error typically occurs in only one of the assemblies.
Are there tools or approaches you recommend for identifying assembly errors after the component assemblies are mapped back to the merged assembly?
I have ONT only Shasta and Flye assemblies and dbg2olc and Masurca hybrid assemblies. I was wondering if there is a suggested strategy for merging them all with quickmerge. Is it as simple as cat the long-read only and cat the hybrid assemblies together and then provide the two files to quickmerge?
Also regarding this helpful tip:
For optimal merging results, identify the major misassemblies (especially translocations and inversions) in the component assemblies and break the contigs at such misassembly boundaries. Alignment of the component assemblies to the merged assembly may help to identify such assembly errors because a specific error typically occurs in only one of the assemblies.
Are there tools or approaches you recommend for identifying assembly errors after the component assemblies are mapped back to the merged assembly?
Thank you!