Coordinates and intervals in graph-based reference genomes

BMC Bioinformatics
Knut D RandGeir K Sandve

Abstract

It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created fro...Continue Reading

References

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Citations

Jan 18, 2018·BMC Genomics·Christine JandrasitsBernhard Y Renard
Feb 20, 2019·PLoS Computational Biology·Ivar GryttenGeir K Sandve
Oct 19, 2017·Current Protocols in Human Genetics·Elizabeth A Worthey
May 27, 2020·Annual Review of Genomics and Human Genetics·Jordan M EizengaErik Garrison
Oct 12, 2018·Bioinformatics·Chakravarthi KanduriGeir Kjetil Sandve
Aug 11, 2019·Genome Biology·Sara BallouzJesse A Gillis
Apr 10, 2021·Briefings in Bioinformatics·Adrien OlivaYassine Souilmi
Oct 14, 2019·F1000Research·Bastien LlamasBen Busby
Aug 21, 2021·Genome Biology·Prashant PandeyCarl Kingsford

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Methods Mentioned

BETA
genotyping

Software Mentioned

iBWA
UCSC Table Browser
GENCODE
OffsetBasedGraph
VG
MEM
SRPRISM
BWA
GSNAP

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