Currently the "urt" (use read tips) switch for Newbler can be enabled so that it is used during all assemblies except for the last one. This doesn't function properly however if assemblies are terminated early because no more reads will map. In this case the final assembly will be made with the "urt" switch enabled, causing the final contigs to have low-quality tips.
samhunter
commented
10 years ago
Currently the "urt" (use read tips) switch for Newbler can be enabled so that it is used during all assemblies except for the last one. This doesn't function properly however if assemblies are terminated early because no more reads will map. In this case the final assembly will be made with the "urt" switch enabled, causing the final contigs to have low-quality tips.