In BioPerl, 'sequence assemblies', such as whole genome shotgun assemblies, are represented as Bio::Assembly::Scaffold objects. They are the objects returned by the 'next_assembly' method of the Bio::Assembly::IO assembly IO 'stream'.
- Bio::Assembly::ScaffoldI for the (unused?) scaffold interface.
- SO terms... tba
A Scaffold object is typically composed of two types of thing:
- Contigs and/or Singlets
- As described in the sequence ontology, contigs and singlets are locatable sub-sequences of the scaffold. In BioPerl, these objects provide access to the underlying sequence reads, their alignments and the alignment consensus sequence, where available.
- A collection of features that provides all additional info about the assembly. Currently I'm not really sure how this object 'works'.
The object methods reflect its composition.