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
Cut Cloud Costs with Google Compute Engine Icon
Cut Cloud Costs with Google Compute Engine

Save up to 91% with Spot VMs and get automatic sustained-use discounts. One free VM per month, plus $300 in credits.

Save on compute costs with Compute Engine. Reduce your batch jobs and workload bill 60-91% with Spot VMs. Compute Engine's committed use offers customers up to 70% savings through sustained use discounts. Plus, you get one free e2-micro VM monthly and $300 credit to start.
Try Compute Engine
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