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Mating-based Overexpression Library Screening in Yeast
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Improving draft genome contiguity with reference-derived in silico mate-pair libraries.

José Horacio Grau1, Thomas Hackl2, Klaus-Peter Koepfli3,4

  • 1Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin. Invalidenstraße 43, 10115. Berlin, Germany.

Gigascience
|April 25, 2018
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Summary
This summary is machine-generated.

We developed Cross-Species Scaffolding, a pipeline to improve genome contiguity using in silico mate-pair libraries. This method enhances genome assembly metrics and gene prediction for better biological resources.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Contiguous genome assemblies are crucial for accurate gene annotation and genomic element analysis.
  • Achieving high contiguity is challenging with low-coverage data or distantly related references.

Purpose of the Study:

  • To develop a novel computational pipeline for improving genome assembly contiguity.
  • To enable high-quality genome assembly from limited sequencing data.

Main Methods:

  • Implemented Cross-Species Scaffolding pipeline utilizing in silico mate-pair libraries.
  • Imported long-range distance information directly into the de novo genome assembly process.

Main Results:

  • Demonstrated significant improvements in genome assembly metrics.
  • Showcased dramatic enhancements in gene prediction accuracy.
  • Successfully assembled two primate genomes using only ~30x shotgun sequencing data.

Conclusions:

  • Cross-Species Scaffolding effectively enhances genome contiguity and quality.
  • The pipeline provides a valuable tool for assembling genomes with limited data.
  • Improved assemblies facilitate more comprehensive genomic research.