SMAP: a versatile approach to read-backed haplotyping in stacked NGS read data

Tom Ruttink; Elisabeth Veeckman; Dries Schaumont; Sabine Van Glabeke; Annelies Haegeman; Hilde Muylle; Isabel Roldán-Ruiz; Jean-Paul Sampoux; Philippe Barre; Stephen Byrne; Jie Kang; Felix Van der Jeugt; Peter Dawyndt

SMAP: a versatile approach to read-backed haplotyping in stacked NGS read data

Tom Ruttink, Elisabeth Veeckman, Dries Schaumont, Sabine Van Glabeke, Annelies Haegeman, Hilde Muylle, Isabel Roldán-Ruiz, Jean-Paul Sampoux, Philippe Barre, Stephen Byrne, Jie Kang, Felix Van der Jeugt , Peter Dawyndt

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Onderzoeksoutput: Bijdrage aan congres › Poster

Uittreksel

We have developed a computational algorithm called "SMAP" (short for Stack Mapping Anchor Points) for read-backed haplotyping in “stacked” NGS reads, applicable to highly multiplex amplicon sequencing (HiPlex) or Genotyping-by-Sequencing (GBS) data. In highly heterozygous species, up to one-third of the loci may display polymorphic read alignments. In addition, SNPs shared between multiple alleles confound analysis of allele frequency shifts. The SMAP algorithm improves allele frequency estimation in pool-Seq data or discrete genotype calls in individuals and groups neighboring SNPs into multi-allelic haplotype markers per locus, thus increasing genetic resolution.

Oorspronkelijke taal	Nederlands
Publicatiestatus	Gepubliceerd - 15-jan.-2020

Andere bestanden en links

https://pag.confex.com/pag/xxviii/meetingapp.cgi/Paper/39472

GA-GENOMICS: Diepduiken in de genomische diversiteit van (meta)populaties
Ruttink, T., Cnops, G., De Campeneere, S., De Loose, M., Debode, J., Goossens, K., Haegeman, A., Heyndrickx, M., Muylle, H., Peiren, N., Rasschaert, G., Robbens, J., Roldán-Ruiz, I., Taverniers, I., Van Coillie, E., Van Glabeke, S., Vandaele, L., De Tender, C., Devriese, L., De Mulder, T., Verwimp, C., Veeckman, E. & Maes, M.
1/10/13 → 31/08/19
Project: Onderzoek

Dit citeren

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title = "SMAP: a versatile approach to read-backed haplotyping in stacked NGS read data",

abstract = "We have developed a computational algorithm called {"}SMAP{"} (short for Stack Mapping Anchor Points) for read-backed haplotyping in “stacked” NGS reads, applicable to highly multiplex amplicon sequencing (HiPlex) or Genotyping-by-Sequencing (GBS) data. In highly heterozygous species, up to one-third of the loci may display polymorphic read alignments. In addition, SNPs shared between multiple alleles confound analysis of allele frequency shifts. The SMAP algorithm improves allele frequency estimation in pool-Seq data or discrete genotype calls in individuals and groups neighboring SNPs into multi-allelic haplotype markers per locus, thus increasing genetic resolution.",

author = "Tom Ruttink and Elisabeth Veeckman and Dries Schaumont and {Van Glabeke}, Sabine and Annelies Haegeman and Hilde Muylle and Isabel Rold{\'a}n-Ruiz and Jean-Paul Sampoux and Philippe Barre and Stephen Byrne and Jie Kang and {Van der Jeugt}, Felix and Peter Dawyndt",

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T1 - SMAP: a versatile approach to read-backed haplotyping in stacked NGS read data

AU - Ruttink, Tom

AU - Veeckman, Elisabeth

AU - Schaumont, Dries

AU - Van Glabeke, Sabine

AU - Haegeman, Annelies

AU - Muylle, Hilde

AU - Roldán-Ruiz, Isabel

AU - Sampoux, Jean-Paul

AU - Barre, Philippe

AU - Byrne, Stephen

AU - Kang, Jie

AU - Van der Jeugt , Felix

AU - Dawyndt, Peter

PY - 2020/1/15

Y1 - 2020/1/15

N2 - We have developed a computational algorithm called "SMAP" (short for Stack Mapping Anchor Points) for read-backed haplotyping in “stacked” NGS reads, applicable to highly multiplex amplicon sequencing (HiPlex) or Genotyping-by-Sequencing (GBS) data. In highly heterozygous species, up to one-third of the loci may display polymorphic read alignments. In addition, SNPs shared between multiple alleles confound analysis of allele frequency shifts. The SMAP algorithm improves allele frequency estimation in pool-Seq data or discrete genotype calls in individuals and groups neighboring SNPs into multi-allelic haplotype markers per locus, thus increasing genetic resolution.

AB - We have developed a computational algorithm called "SMAP" (short for Stack Mapping Anchor Points) for read-backed haplotyping in “stacked” NGS reads, applicable to highly multiplex amplicon sequencing (HiPlex) or Genotyping-by-Sequencing (GBS) data. In highly heterozygous species, up to one-third of the loci may display polymorphic read alignments. In addition, SNPs shared between multiple alleles confound analysis of allele frequency shifts. The SMAP algorithm improves allele frequency estimation in pool-Seq data or discrete genotype calls in individuals and groups neighboring SNPs into multi-allelic haplotype markers per locus, thus increasing genetic resolution.

UR - https://pag.confex.com/pag/xxviii/meetingapp.cgi/Paper/39472

M3 - Poster

ER -

SMAP: a versatile approach to read-backed haplotyping in stacked NGS read data

Uittreksel

Andere bestanden en links

Projecten

GA-GENOMICS: Diepduiken in de genomische diversiteit van (meta)populaties

Dit citeren