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Bioinformatics. 2019 Aug 1. pii: btz597. doi: 10.1093/bioinformatics/btz597. [Epub ahead of print]

Sequence tube maps: making graph genomes intuitive to commuters.

Author information

1
UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
2
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

Abstract

MOTIVATION:

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 analysed. However, their adoption in genomic research is slow, in part because of the cognitive difficulty in interpreting graphs.

RESULTS:

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.

AVAILABILITY:

Code: https://github.com/vgteam/sequenceTubeMap.

DEMONSTRATION:

https://vgteam.github.io/sequenceTubeMap/.

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