Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 72,924 bioRxiv papers from 317,458 authors.

Sequence variation aware genome references and read mapping with the variation graph toolkit

By Erik Garrison, Jouni Sirén, Adam M. Novak, Glenn Hickey, Jordan M Eizenga, Eric T. Dawson, William Jones, Michael F Lin, Benedict Paten, Richard Durbin

Posted 15 Dec 2017
bioRxiv DOI: 10.1101/234856 (published DOI: 10.1038/nbt.4227)

Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references are fundamentally limited in that they represent only one version of each locus, whereas the population may contain multiple variants. When the reference represents an individual's genome poorly, it can impact read mapping and introduce bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation, including large scale structural variation such as inversions and duplications. Equivalent structures are produced by de novo genome assemblers. Here we present vg, a toolkit of computational methods for creating, manipulating, and utilizing these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays, with improved accuracy over alignment to a linear reference, creating data structures to support downstream variant calling and genotyping. These capabilities make using variation graphs as reference structures for DNA sequencing practical at the scale of vertebrate genomes, or at the topological complexity of new species assemblies.

Download data

  • Downloaded 3,529 times
  • Download rankings, all-time:
    • Site-wide: 965 out of 72,915
    • In genomics: 238 out of 4,843
  • Year to date:
    • Site-wide: 13,437 out of 72,915
  • Since beginning of last month:
    • Site-wide: 13,437 out of 72,915

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News