454 Assembled Reads

Question

[Janake]

I have 454 assembled contigs, Isotigs and singletons. The core facility that we used has done this for us, using Newbler. Do I still need to get rid of any adapter sequences or can I use these data directly for other analyses? In addition, how can I combine Isotigs, contigs and singltons?

[User 59]

The adapter sequences should have been removed prior to assembly.

Answer 1

[Istvan Albert]

As Daniel mentioned in the comment the adapters must have been already removed to allow for assembly. Your next step depends on the specifics of your data and goals. For example you could use CD-HIT to cluster the isotigs.