Module:Bio::Assembly::Scaffold

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Pdoc documentation: Bio::Assembly::Scaffold	CPAN documentation: Bio::Assembly::Scaffold

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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'.

See also:

• Bio::Assembly::ScaffoldI for the (unused?) scaffold interface.
• SO terms... tba

Implementation overview

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.

Bio::Annotation::Collection 

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.