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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.
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Evolution of Microbial Genome

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Genomics

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Related Experiment Video

Updated: May 16, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

High-throughput microbial population genomics using the Cortex variation assembler.

Zamin Iqbal1, Isaac Turner, Gil McVean

  • 1Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK. zam@well.ox.ac.uk

Bioinformatics (Oxford, England)
|November 23, 2012
PubMed
Summary
This summary is machine-generated.

Cortex software enables de novo assembly and genetic variation analysis for multiple samples without a reference genome. This tool discovers and genotypes various genetic variations, simplifying microbial sample analysis and accelerating comparisons.

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Last Updated: May 16, 2026

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Analysis of genetic variation is crucial for understanding biological systems.
  • De novo assembly is a key technique for genome analysis, especially without a reference genome.

Purpose of the Study:

  • To develop a software package, Cortex, for analyzing genetic variation through de novo assembly of multiple samples.
  • To enable direct sample comparison and incorporate discovery and genotyping of various genetic variations in a single framework.

Main Methods:

  • Developed the Cortex software package for de novo assembly and genetic variation analysis.
  • Introduced pipelines for simplified microbial sample analysis and increased discovery power.
  • Enabled rapid comparison of new samples against a graph of known species sequence and variation.

Main Results:

  • Demonstrated the software's ease-of-use and power by reproducing results from existing studies.
  • Successfully incorporated discovery and genotyping of single-nucleotide polymorphisms, indels, and larger events.
  • Facilitated direct comparison of multiple samples without relying on a reference genome.

Conclusions:

  • Cortex provides a powerful and user-friendly framework for analyzing genetic variation via de novo assembly.
  • The software simplifies microbial genomics and enhances the discovery of genetic variants.
  • Cortex is effective for both long and short read data, offering a versatile tool for genomic research.