Lep-MAP: fast and accurate linkage map construction for large SNP datasets

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Motivation: Current high-throughput sequencing technologies allow cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for hundreds of samples. However, the tools that are currently available for constructing linkage maps are not well suited for large datasets. Linkage maps of large datasets would be helpful in de novo genome assembly by facilitating comprehensive genome validation and refinement by enabling chimeric scaffold detection, as well as in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other complex genomic data analyses.

Results: We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data. Lep-MAP is fast and memory efficient and largely automated, requiring minimal user interaction. It uses simultaneously data on multiple outbred families and can increase linkage map accuracy by taking into account achiasmatic meiosis, a special feature of Lepidoptera and some other taxa with no recombination in one sex (no recombination in females in Lepidoptera). We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs. The data were generated with a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol, which is described in the online supplementary material.

Availability and implementation: Java source code under GNU general public license with the compiled classes and the datasets are available from http://sourceforge.net/users/lep-map.

Contact: pasi.rastas@helsinki.fi

Supplementary information: Supplementary data are available at Bioinformatics online.
Original languageEnglish
JournalBioinformatics
Volume29
Issue number24
Pages (from-to)3128-3134
Number of pages7
ISSN1367-4803
DOIs
Publication statusPublished - 2013
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 1184 Genetics, developmental biology, physiology
  • 113 Computer and information sciences

Cite this

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abstract = "Motivation: Current high-throughput sequencing technologies allow cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for hundreds of samples. However, the tools that are currently available for constructing linkage maps are not well suited for large datasets. Linkage maps of large datasets would be helpful in de novo genome assembly by facilitating comprehensive genome validation and refinement by enabling chimeric scaffold detection, as well as in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other complex genomic data analyses.Results: We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data. Lep-MAP is fast and memory efficient and largely automated, requiring minimal user interaction. It uses simultaneously data on multiple outbred families and can increase linkage map accuracy by taking into account achiasmatic meiosis, a special feature of Lepidoptera and some other taxa with no recombination in one sex (no recombination in females in Lepidoptera). We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs. The data were generated with a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol, which is described in the online supplementary material.Availability and implementation: Java source code under GNU general public license with the compiled classes and the datasets are available from http://sourceforge.net/users/lep-map.Contact: pasi.rastas@helsinki.fiSupplementary information: Supplementary data are available at Bioinformatics online.",
keywords = "1184 Genetics, developmental biology, physiology, 113 Computer and information sciences",
author = "Pasi Rastas and Lars Paulin and Ilkka Hanski and Lehtonen, {Rainer Juhani} and Petri Auvinen",
year = "2013",
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Lep-MAP: fast and accurate linkage map construction for large SNP datasets. / Rastas, Pasi; Paulin, Lars; Hanski, Ilkka; Lehtonen, Rainer Juhani; Auvinen, Petri.

In: Bioinformatics, Vol. 29, No. 24, 2013, p. 3128-3134.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Lep-MAP: fast and accurate linkage map construction for large SNP datasets

AU - Rastas, Pasi

AU - Paulin, Lars

AU - Hanski, Ilkka

AU - Lehtonen, Rainer Juhani

AU - Auvinen, Petri

PY - 2013

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N2 - Motivation: Current high-throughput sequencing technologies allow cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for hundreds of samples. However, the tools that are currently available for constructing linkage maps are not well suited for large datasets. Linkage maps of large datasets would be helpful in de novo genome assembly by facilitating comprehensive genome validation and refinement by enabling chimeric scaffold detection, as well as in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other complex genomic data analyses.Results: We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data. Lep-MAP is fast and memory efficient and largely automated, requiring minimal user interaction. It uses simultaneously data on multiple outbred families and can increase linkage map accuracy by taking into account achiasmatic meiosis, a special feature of Lepidoptera and some other taxa with no recombination in one sex (no recombination in females in Lepidoptera). We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs. The data were generated with a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol, which is described in the online supplementary material.Availability and implementation: Java source code under GNU general public license with the compiled classes and the datasets are available from http://sourceforge.net/users/lep-map.Contact: pasi.rastas@helsinki.fiSupplementary information: Supplementary data are available at Bioinformatics online.

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DO - 10.1093/bioinformatics/btt563

M3 - Article

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SP - 3128

EP - 3134

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 24

ER -