Sequence tube maps: making graph genomes intuitive to commuters.

Bioinformatics
Wolfgang BeyerDaniel R Zerbino

Abstract

Compared to traditional haploid reference genomes, graph genomes are an efficient and compact data structure for storing multiple genomic sequences, for storing polymorphisms or for mapping sequencing reads with greater sensitivity. Further, graphs are well-studied computer science objects that can be efficiently analyzed. However, their adoption in genomic research is slow, in part because of the cognitive difficulty in interpreting graphs. We present an intuitive graphical representation for graph genomes that re-uses well-honed techniques developed to display public transport networks, and demonstrate it as a web tool. Code: https://github.com/vgteam/sequenceTubeMap. https://vgteam.github.io/sequenceTubeMap/. Supplementary data are available at Bioinformatics online.

References

Aug 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Paul Medvedev, Michael Brudno
Oct 17, 2009·IEEE Transactions on Visualization and Computer Graphics·Cydney B NielsenSteven J M Jones
Jun 24, 2015·Bioinformatics·Ryan R WickKathryn E Holt
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Apr 1, 2017·Genome Research·Benedict PatenErik Garrison

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Citations

May 27, 2020·Annual Review of Genomics and Human Genetics·Jordan M EizengaErik Garrison
Nov 7, 2019·BMC Bioinformatics·Toshiyuki T YokoyamaMasahiro Kasahara
Apr 14, 2021·Annual Review of Plant Biology·Li LeiJohn P Vogel
Oct 4, 2021·Bioinformatics·Éloi DurantMathieu Rouard

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Software Mentioned

Tube Maps
SequenceTubeMap
vg

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