Browsing by Author "Burgin, Josephine"
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Open Access CRAMER: A lightweight, highly customisable web-based genome browser supporting multiple visualisation instances(Oxford University Press, 2020-02-28) Anastasiadi, Maria; Bragin, E.; Biojoux, P.; Ahamed, A.; Burgin, Josephine; de Castro Cogle, K.; Llaneza-Lago, S.; Muvunyi, R.; Scislak, M.; Aktan, I.; Molitor, Corentin; Kurowski, Tomasz J.; Mohareb, Fady R.In recent years the ability to generate genomic data has increased dramatically along with the demand for easily personalised and customisable genome browsers for effective visualisation of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provide means for creating multiple visualisation instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customisable web application for interactive visualisation of genomic data. Once deployed, CRAMER supports seamless creation of multiple visualisation instances in parallel while allowing users to control and customise multiple tracks. The application is deployed on a Node.js server and is supported by a MongoDB database which stored all customisations made by the users allowing quick navigation between instances. Currently, the browser supports visualising a large number of file formats for genome annotation, variant calling, reads coverage and gene expression. Additionally, the browser supports direct Javascript coding for personalised tracks, providing a whole new level of customisation both functionally and visually. Tracks can be added via direct file upload or processed in real-time via links to files stored remotely on an FTP repository. Furthermore, additional tracks can be added by users via simple drag and drop to an existing visualisation instance.Item Open Access MapOptics: A light-weight, cross-platform visualisation tool for optical mapping alignment(Oxford University Press, 2018-12-07) Burgin, Josephine; Molitor, Corentin; Mohareb, Fady R.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 visualisation are limited to use on a Windows operating system or are developed initially for visualising large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualise 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.