Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N's and small overlaps are aligned with Needleman–Wunsch algorithm and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.


(c) Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.
Please cite: "Combining de novo and reference-guided assembly with Scaffold_builder", Source Code for Biology and Medicine 2013.

Features

  • scaffold
  • draft genome
  • bioinformatics

Project Samples

Flow diagram of the Scaffold_builder script.

Project Activity

See All Activity >

Follow Scaffold_Builder

Scaffold_Builder Web Site

Other Useful Business Software
Gemini 3 and 200+ AI Models on One Platform Icon
Gemini 3 and 200+ AI Models on One Platform

Access Google's best plus Claude, Llama, and Gemma. Fine-tune and deploy from one console.

Build generative AI apps with Vertex AI. Switch between models without switching platforms.
Start Free
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of Scaffold_Builder!

Additional Project Details

User Interface

Command-line, Web-based

Programming Language

Python

Registered

2011-10-01
Report inappropriate content