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Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data.

Pasi Rastas1,2

  • 1Department of Zoology, Butterfly Genetics Group, University of Cambridge, Cambridge, UK.

Bioinformatics (Oxford, England)
|October 17, 2017
PubMed
Summary

Lep-MAP3 is new software for creating accurate linkage maps from whole genome sequencing data. It efficiently handles large, low-coverage datasets, improving genome assembly validation and refinement with millions of markers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate linkage maps are crucial for various genomic analyses, including family-based studies, quantitative trait locus mapping, and genome synteny analysis.
  • Linkage mapping is essential for detecting errors in de novo genome assemblies and orienting contigs within chromosomes.
  • Existing tools struggle with large, low-coverage whole genome sequencing datasets, hindering comprehensive genomic analyses.

Purpose of the Study:

  • To develop and present Lep-MAP3, a novel software tool for constructing high-throughput linkage maps from whole genome sequencing data.
  • To enable cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for thousands of individuals.
  • To facilitate comprehensive validation and refinement of de novo genome assemblies using linkage mapping.

Main Methods:

  • Lep-MAP3 employs advanced algorithms to analyze high-throughput whole genome sequencing data, including low-coverage datasets.
  • The software reduces the need for extensive data filtering and curation, simplifying the mapping process.
  • Performance is evaluated using simulated data and real data from the Red postman butterfly (Heliconius erato).

Main Results:

  • Lep-MAP3 demonstrates high accuracy and speed, outperforming existing software on simulated data.
  • The software performs well even on datasets with as low as 5x sequencing coverage.
  • De novo linkage maps with nearly 3 million markers were constructed using 7-12x whole-genome data from Heliconius erato.

Conclusions:

  • Lep-MAP3 is a powerful and efficient tool for generating dense linkage maps from large-scale, low-coverage whole genome sequencing data.
  • The software significantly reduces manual effort and improves the quality of linkage maps, even with challenging datasets.
  • Lep-MAP3 enables more comprehensive genomic analyses, including robust validation and refinement of genome assemblies.