Sequence tube maps: making graph genomes intuitive to commuters.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
15 12 2019
15 12 2019
Historique:
received:
25
03
2019
revised:
27
06
2019
accepted:
26
07
2019
pubmed:
2
8
2019
medline:
1
7
2020
entrez:
2
8
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31368484
pii: 5542397
doi: 10.1093/bioinformatics/btz597
pmc: PMC6954646
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5318-5320Subventions
Organisme : Wellcome Trust
ID : WT108749/Z/15/Z
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : U01 HL137183
Pays : United States
Organisme : Wellcome Trust
ID : 201535/Z/16/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WT201535/Z/16/Z
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U54 HG007990
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
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