Reference-based scaffolding and finishing methods can be detrimental to the assembly if the reference sequence is too divergent from the assembled contigs. Adding a check for %id and %age of contigs aligned to reference prior to these stages should prevent such situations arising
jamesabbott
commented
7 years ago
Reference-based scaffolding and finishing methods can be detrimental to the assembly if the reference sequence is too divergent from the assembled contigs. Adding a check for %id and %age of contigs aligned to reference prior to these stages should prevent such situations arising