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scaffold_builder

The abundance of repeat elements in genomes can impede the assembly of a single sequence. The tool Scaffold_builder was designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.

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scaffold_builder classification

scaffold_builder specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Python
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes

scaffold_builder distribution

versioning

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scaffold_builder forum

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No open topic.

scaffold_builder classification

scaffold_builder specifications

Interface:
Web user interface
Programming languages:
Python
Stability:
Stable
Restrictions to use:
None
Computer skills:
Basic
Maintained:
Yes

scaffold_builder support

Maintainer

  • Robert Edwards <>
  • Robert Edwards <>

Credits

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Publications

Institution(s)

Computational Science Research Center, San Diego State University, San Diego, CA, USA

Link to literature

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