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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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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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FGMP: assessing fungal genome completeness.

Ousmane H Cissé1,2, Jason E Stajich3

  • 1Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA, 92521, USA. ousmanecis@gmail.com.

BMC Bioinformatics
|April 17, 2019
PubMed
Summary

We developed the Fungal Genome Mapping Project (FGMP) to accurately assess fungal genome completeness. This tool aids researchers by providing reliable genome quality metrics, especially for non-model organisms, reducing sequencing costs.

Keywords:
AssemblyConserved elementsGene model

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Area of Science:

  • Genomics
  • Bioinformatics
  • Mycology

Background:

  • High-throughput DNA sequencing enables genetic research beyond model organisms.
  • Variable genome assembly quality hinders comparative genomics and interpretation.
  • Uncertainty in genome completeness limits studies on gene loss.

Purpose of the Study:

  • To introduce a computational framework and resource for assessing fungal genome completeness.
  • To provide a reliable method for evaluating the quality of fungal genome assemblies.

Main Methods:

  • Developed the Fungal Genome Mapping Project (FGMP) computational framework.
  • Utilized evolutionary conserved protein and DNA elements for assessment.
  • Applied the framework to 246 fungal genome assemblies and compared with existing methods.

Main Results:

  • FGMP accurately quantifies the completeness level of fungal genomic data.
  • Demonstrated FGMP's utility across various genomic data types.
  • Analyzed assembly improvements/degradations in 57 updated fungal genomes.

Conclusions:

  • FGMP is an accurate tool for fungal genome completion assessment.
  • FGMP is valuable for non-model organisms lacking reference genomes.
  • Direct application to unassembled reads can reduce genome sequencing costs.