StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
28 03 2022
28 03 2022
Historique:
received:
22
08
2021
revised:
23
11
2021
accepted:
07
01
2022
pubmed:
13
1
2022
medline:
19
11
2022
entrez:
12
1
2022
Statut:
ppublish
Résumé
The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we introduce StainedGlass, which can generate publication-quality figures and interactive visualizations that depict the identity and orientation of multi-megabase tandem repeat structures at a genome-wide scale. The tool can rapidly reveal higher-order structures and improve the inference of evolutionary history for some of the most complex regions of genomes. StainedGlass is implemented using Snakemake and available open source under the MIT license at https://mrvollger.github.io/StainedGlass/. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 35020798
pii: 6502275
doi: 10.1093/bioinformatics/btac018
pmc: PMC8963321
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Intramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
2049-2051Subventions
Organisme : NHGRI NIH HHS
ID : U01 HG010973
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG010971
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG007497
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG002385
Pays : United States
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.