[shaojingwang]

Use the -rip option when starting the assembly, or edit 454AssemblyProject.xml
and set <ripMode>true</ripMode>. Newbler should include reads in the assembly once once.

Truly said, it does not work well for me (maybe Roche only promises that no 2 read appear in a same contig, not isotig, maybe that is the point), I still have 2 isotigs with same reads included, so consed later on barfs on me that it cannot import "contigs" (in its terminology) because of duplicated read names.

Excuse me, I want to know, for cDNA assembly, reads should be assembled to multiple contigs or not? If not, in what situation reads should be assembled to multiple contigs? urgent for answer...