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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Related Experiment Video

Updated: May 22, 2026

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Scaffolder - software for manual genome scaffolding.

Michael D Barton1, Hazel A Barton

  • 1Biology Department, The University of Akron, Akron, OH, 44325-3908, USA. mail@michaelbarton.me.uk.

Source Code for Biology and Medicine
|May 30, 2012
PubMed
Summary

Scaffolder software simplifies genome assembly by enabling reproducible and editable genome builds. This tool facilitates gap-filling and sequence joining, improving genome project workflows.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing data assembly often yields fragmented genomic sequences.
  • Scaffolding, the process of joining these sequences and filling gaps, is complex and hinders reproducibility.
  • Manual editing of large nucleotide sequences is time-consuming and error-prone.

Purpose of the Study:

  • To develop user-friendly software for reproducible genome scaffolding.
  • To provide a method for easily editing and managing genome builds.

Main Methods:

  • Scaffolder software implemented in Ruby and installable via RubyGems.
  • Genome scaffolds defined using human- and machine-readable YAML format.
  • Command-line binaries and comprehensive documentation provided.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Related Experiment Videos

Last Updated: May 22, 2026

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Main Results:

  • Scaffolder allows genome construction definition via simple syntax.
  • Supports specification of unknown regions and gap-filling with additional sequences.
  • File-based definition enhances reproducibility and editability over FASTA sequences.

Conclusions:

  • Scaffolder offers an easy-to-use solution for genome scaffolding.
  • Promotes reproducibility and continuous development in genome projects.
  • Available at http://next.gs.