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

Project Activity

See All Activity >

Follow Scaffold_Builder

Scaffold_Builder Web Site

Other Useful Business Software
Gen AI apps are built with MongoDB Atlas Icon
Gen AI apps are built with MongoDB Atlas

Build gen AI apps with an all-in-one modern database: MongoDB Atlas

MongoDB Atlas provides built-in vector search and a flexible document model so developers can build, scale, and run gen AI apps without stitching together multiple databases. From LLM integration to semantic search, Atlas simplifies your AI architecture—and it’s free to get started.
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

Web-based, Command-line

Programming Language

Python

Registered

2011-10-01