MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 08 2019
01 08 2019
Historique:
received:
16
09
2018
revised:
27
11
2018
accepted:
06
12
2018
pubmed:
12
12
2018
medline:
17
6
2020
entrez:
12
12
2018
Statut:
ppublish
Résumé
Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the assembly to a genomic map. However, currently, tools for visualization are limited to use on a Windows operating system or are developed initially for visualizing large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualize and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments. It provides a fast, simple alternative to the large optical mapping analysis programs currently available for this area of research. MapOptics is implemented in Java 1.8 and released under an MIT licence. MapOptics can be downloaded from https://github.com/FadyMohareb/mapoptics and run on any standard desktop computer equipped with a Java Virtual Machine (JVM). Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 30535283
pii: 5232997
doi: 10.1093/bioinformatics/bty1013
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2671-2673Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/L011611/1
Pays : United Kingdom
Informations de copyright
© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.