From CSBLwiki

Tips for Newbler de novo assembler

• 454Scaffolds: Contigs with gaps or contigs longer than 2000bp
• 454AllContigs: If there are multi copy contigs, the Newbler make them island.
  • gapResolution: can cover this problem by local assembly.
  • We can manually check with 454PairStatus.txt file.
  • It is important to know which contig is multicopy and how many it(orgarnism) has.