Genome graphs and the evolution of genome inference

By Benedict Paten, Adam M. Novak, Jordan M. Eizenga, Garrison Erik. bioRxiv, 2017

314 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a4de101024c6bb0f02b4e1560b74048835df9c5d

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Citations in the corpus

Genome evolution across 1,011 Saccharomyces cerevisiae isolates (2018, unknown): “The availability of end-to-end genome assemblies will enable the organization of such a dataset with genome graphs 50 .”
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs (2022, background): “More recently, the representation of biological sequences has been expressed under the conceptual framework of graph theory [7].”
A draft human pangenome reference (2022, methodology): “Constructing a draft pangenome We use a sequence graph representation for pangenomes (Eizenga et al., 2020; Paten et al., 2017) in which nodes correspond to segments of DNA.”
What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species (2018, background): “Thanks to remarkable advances in sequencing technologies and de novo genome assembly (Alkhateeb & Rueda, 2017; Jackman et al., 2017; Kamath et al., 2017; Paten et al., 2017; Vaser et al., 2017; Worley, 2017), it is no longer the case that the availability of a closely related model species and refer”
Variation graph toolkit improves read mapping by representing genetic variation in the reference (2018, unknown): “Overall vg performs at least as well as bwa mem even on reference-derived reads, and substantially better on reads containing non-reference variants.”