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Graph genomes

From Figure 2, Schatz et al. Genome Biology 2012;13(4):243.

The first reference genome sequences were entirely linear from a single or few individuals, but such a representation is not sufficient for encompassing all of the genomic variation present in a population. The human reference GRCh37 adopted a graph-based representation, by introducing the concept of alternative loci, which was expanded in GRCh38. Uptake of these graphical representations has been slow, in part because of a lack of tools to process the data in this form. 

Genome Biology presents a collection of articles on Graph Genomes, guest edited by Michael Schatz (Johns Hopkins University, USA). 

  1. We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which an...

    Authors: Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst and Zamin Iqbal
    Citation: Genome Biology 2021 22:267
  2. Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, ...

    Authors: Prashant Pandey, Yinjie Gao and Carl Kingsford
    Citation: Genome Biology 2021 22:231
  3. During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short ...

    Authors: Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica and Richard Durbin
    Citation: Genome Biology 2020 21:250
  4. Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the auto...

    Authors: Gerry Tonkin-Hill, Neil MacAlasdair, Christopher Ruis, Aaron Weimann, Gal Horesh, John A. Lees, Rebecca A. Gladstone, Stephanie Lo, Christopher Beaudoin, R. Andres Floto, Simon D.W. Frost, Jukka Corander, Stephen D. Bentley and Julian Parkhill
    Citation: Genome Biology 2020 21:180
  5. The practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of in...

    Authors: Tom Mokveld, Jasper Linthorst, Zaid Al-Ars, Henne Holstege and Marcel Reinders
    Citation: Genome Biology 2020 21:65
  6. Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide a...

    Authors: Glenn Hickey, David Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak and Benedict Paten
    Citation: Genome Biology 2020 21:35
  7. Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an a...

    Authors: Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M. Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David R. Bentley, Michael C. Schatz, Fritz J. Sedlazeck and Michael A. Eberle
    Citation: Genome Biology 2019 20:291
  8. There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a v...

    Authors: Jacob Pritt, Nae-Chyun Chen and Ben Langmead
    Citation: Genome Biology 2018 19:220