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Genome graphs and the evolution of genome inference
The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762/ https://www.ncbi.nlm.nih.gov/pubmed/28360232 http://dx.doi.org/10.1101/gr.214155.116 |
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author | Paten, Benedict Novak, Adam M. Eizenga, Jordan M. Garrison, Erik |
author_facet | Paten, Benedict Novak, Adam M. Eizenga, Jordan M. Garrison, Erik |
author_sort | Paten, Benedict |
collection | PubMed |
description | The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph-based models. Here, we survey various projects underway to build and apply these graph-based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce. |
format | Online Article Text |
id | pubmed-5411762 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-54117622017-05-16 Genome graphs and the evolution of genome inference Paten, Benedict Novak, Adam M. Eizenga, Jordan M. Garrison, Erik Genome Res Review The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph-based models. Here, we survey various projects underway to build and apply these graph-based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce. Cold Spring Harbor Laboratory Press 2017-05 /pmc/articles/PMC5411762/ /pubmed/28360232 http://dx.doi.org/10.1101/gr.214155.116 Text en © 2017 Paten et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Review Paten, Benedict Novak, Adam M. Eizenga, Jordan M. Garrison, Erik Genome graphs and the evolution of genome inference |
title | Genome graphs and the evolution of genome inference |
title_full | Genome graphs and the evolution of genome inference |
title_fullStr | Genome graphs and the evolution of genome inference |
title_full_unstemmed | Genome graphs and the evolution of genome inference |
title_short | Genome graphs and the evolution of genome inference |
title_sort | genome graphs and the evolution of genome inference |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762/ https://www.ncbi.nlm.nih.gov/pubmed/28360232 http://dx.doi.org/10.1101/gr.214155.116 |
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